scholarly journals Dysregulation of post-transcriptional modification by copy number variable microRNAs in schizophrenia with enhanced glycation stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Akane Yoshikawa ◽  
Itaru Kushima ◽  
Mitsuhiro Miyashita ◽  
Kazuya Toriumi ◽  
Kazuhiro Suzuki ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Copy Number ◽  
Mirna Target ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Synaptic Function ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Genome Wide

AbstractPreviously, we identified a subpopulation of schizophrenia (SCZ) showing increased levels of plasma pentosidine, a marker of glycation and oxidative stress. However, its causative genetic factors remain largely unknown. Recently, it has been suggested that dysregulated posttranslational modification by copy number variable microRNAs (CNV-miRNAs) may contribute to the etiology of SCZ. Here, an integrative genome-wide CNV-miRNA analysis was performed to investigate the etiology of SCZ with accumulated plasma pentosidine (PEN-SCZ). The number of CNV-miRNAs and the gene ontology (GO) in the context of miRNAs within CNVs were compared between PEN-SCZ and non-PEN-SCZ groups. Gene set enrichment analysis of miRNA target genes was further performed to evaluate the pathways affected in PEN-SCZ. We show that miRNAs were significantly enriched within CNVs in the PEN-SCZ versus non-PEN-SCZ groups (p = 0.032). Of note, as per GO analysis, the dysregulated neurodevelopmental events in the two groups may have different origins. Additionally, gene set enrichment analysis of miRNA target genes revealed that miRNAs involved in glycation/oxidative stress and synaptic neurotransmission, especially glutamate/GABA receptor signaling, were possibly affected in PEN-SCZ. To the best of our knowledge, this is the first genome-wide CNV-miRNA study suggesting the role of CNV-miRNAs in the etiology of PEN-SCZ, through effects on genes related to glycation/oxidative stress and synaptic function. Our findings provide supportive evidence that glycation/oxidative stress possibly caused by genetic defects related to the posttranscriptional modification may lead to synaptic dysfunction. Therefore, targeting miRNAs may be one of the promising approaches for the treatment of PEN-SCZ.

scholarly journals Genome-wide association analysis of hippocampal volume identifies enrichment of neurogenesis-related pathways

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Emrin Horgusluoglu-Moloch ◽  
◽  
Shannon L. Risacher ◽  
Paul K. Crane ◽  
Derrek Hibar ◽  
...  
Keyword(s):  
Association Analysis ◽  
Adult Neurogenesis ◽  
Enrichment Analysis ◽  
Hippocampal Volume ◽  
Imaging Genetics ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Genome Wide

Abstract Adult neurogenesis occurs in the dentate gyrus of the hippocampus during adulthood and contributes to sustaining the hippocampal formation. To investigate whether neurogenesis-related pathways are associated with hippocampal volume, we performed gene-set enrichment analysis using summary statistics from a large-scale genome-wide association study (N = 13,163) of hippocampal volume from the Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) Consortium and two year hippocampal volume changes from baseline in cognitively normal individuals from Alzheimer’s Disease Neuroimaging Initiative Cohort (ADNI). Gene-set enrichment analysis of hippocampal volume identified 44 significantly enriched biological pathways (FDR corrected p-value < 0.05), of which 38 pathways were related to neurogenesis-related processes including neurogenesis, generation of new neurons, neuronal development, and neuronal migration and differentiation. For genes highly represented in the significantly enriched neurogenesis-related pathways, gene-based association analysis identified TESC, ACVR1, MSRB3, and DPP4 as significantly associated with hippocampal volume. Furthermore, co-expression network-based functional analysis of gene expression data in the hippocampal subfields, CA1 and CA3, from 32 normal controls showed that distinct co-expression modules were mostly enriched in neurogenesis related pathways. Our results suggest that neurogenesis-related pathways may be enriched for hippocampal volume and that hippocampal volume may serve as a potential phenotype for the investigation of human adult neurogenesis.

scholarly journals Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association Studies

2021 ◽  
Vol 12 ◽  
Author(s):  
Michal Marczyk ◽  
Agnieszka Macioszek ◽  
Joanna Tobiasz ◽  
Joanna Polanska ◽  
Joanna Zyla
Keyword(s):  
Association Studies ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Gene Set Analysis ◽  
Genome Wide Association Studies ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Genome Wide ◽  
The Impact

A typical genome-wide association study (GWAS) analyzes millions of single-nucleotide polymorphisms (SNPs), several of which are in a region of the same gene. To conduct gene set analysis (GSA), information from SNPs needs to be unified at the gene level. A widely used practice is to use only the most relevant SNP per gene; however, there are other methods of integration that could be applied here. Also, the problem of nonrandom association of alleles at two or more loci is often neglected. Here, we tested the impact of incorporation of different integrations and linkage disequilibrium (LD) correction on the performance of several GSA methods. Matched normal and breast cancer samples from The Cancer Genome Atlas database were used to evaluate the performance of six GSA algorithms: Coincident Extreme Ranks in Numerical Observations (CERNO), Gene Set Enrichment Analysis (GSEA), GSEA-SNP, improved GSEA for GWAS (i-GSEA4GWAS), Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA), and Over-Representation Analysis (ORA). Association of SNPs to phenotype was calculated using modified McNemar’s test. Results for SNPs mapped to the same gene were integrated using Fisher and Stouffer methods and compared with the minimum p-value method. Four common measures were used to quantify the performance of all combinations of methods. Results of GSA analysis on GWAS were compared to the one performed on gene expression data. Comparing all evaluation metrics across different GSA algorithms, integrations, and LD correction, we highlighted CERNO, and MAGENTA with Stouffer as the most efficient. Applying LD correction increased prioritization and specificity of enrichment outcomes for all tested algorithms. When Fisher or Stouffer were used with LD, sensitivity and reproducibility were also better. Using any integration method was beneficial in comparison with a minimum p-value method in specific combinations. The correlation between GSA results from genomic and transcriptomic level was the highest when Stouffer integration was combined with LD correction. We thoroughly evaluated different approaches to GSA in GWAS in terms of performance to guide others to select the most effective combinations. We showed that LD correction and Stouffer integration could increase the performance of enrichment analysis and encourage the usage of these techniques.

scholarly journals Interaction with the DNA Binding Domain of MLL and a Small Molecular Drug Induces Proteolysis of MLL-Fusion Proteins and Ablates Leukemic Stem Cell Activity

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1549-1549
Author(s):  
Jasper de Boer ◽  
Sandra Cantilena
Keyword(s):  
Fusion Protein ◽  
Cell Lines ◽  
Fusion Proteins ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Self Renewal ◽  
Gene Set ◽  
Cellular Machinery

Abstract Introduction Leukemias harbouring 11q23 abnormalities causing mixed-lineage leukaemia gene (MLL) rearrangements are associated with poor clinical outcomes. Despite being an aggressive leukaemia, the MLL rearranged infant ALL has among the lowest mutation rates reported for any cancer. This means that to improve survival for patients with this aggressive leukaemia we need drugs that target the abnormal proteins produced by the MLL fusion gene or that interact with the abnormal MLL fusion protein to shut down the cellular machinery that drives these leukemias. Indeed, targeting MLL fusion dependent gene pathways has become a major focus. Our previous studies have shown that inhibition of MLL-fusions, in a conditional mouse model of MLL-ENL driven acute myeloid leukaemia, resulted in a block in self-renewal of the leukemic cells and ablated the leukaemia in the mice. This led us to hypothesise that if, we could achieve pharmacological inactivation of the MLL fusion proteins, we could achieve improved clinical outcomes. To achieve this, we set out a drug screening programme in acute leukaemia with the aim to discover drugs that can inactivate MLL-fusion oncoproteins. Results Our drug discovery pipeline screened clinical approved drugs for their ability to inhibit the function of the MLL fusion protein. This lead to the discovery of a drug that interacts with the DNA binding domain within the MLL fusion protein. This interaction destabilises the MLL fusion protein so that the fusion protein gets degraded within 24 hours of addition of the drug. So far, we have shown that we can inhibit and induce the degradation of MLL-AF9, MLL-AF6 and MLL-AF4 (and WT MLL) in the human MLL rearranged cell lines (THP-1, SHI-I and MV4-11), in primary immortalized cells in which the MLL-AF9 is overexpressed from a lentiviral backbone and in patient derived leukemic samples. Inactivation/degradation of the MLL fusion protein should shut down the cellular machinery that drives these leukemias. It is well established that MLL-fusions lead to abhorrent upregulation of its target genes HOXA9, MEIS1 and c-MYB. Treatment of MLL rearranged cells resulted in the downregulation of these MLL-fusion target genes within 24hrs of addition of the drug. Furthermore, Gene Set Enrichment Analysis of drug treated MLL-AF9 cells showed strong negative enrichment to various published MLL fusion target gene sets. Inactivation of MLL fusion protein should also result in block in self-renewal as we have previously shown in our conditional mouse model. Indeed, Gene Set Enrichment Analysis showed negative enrichment to published Leukemic Stem Cell gene set. To analyse the impact of drug treatment on self-renewal, we used a well-established self-renewal assay, whereby self-renewal is assessed by their ability to form colonies derived from single cells in methylcellulose. While treatment had no significant impact on the colony formation of CD34 positive cord blood progenitors, the drug was able to block the colony formation ability of MLL rearranged cell lines while only slowing a slight reduction in in the colony numbers of non MLL rearranged cell lines. Conclusion Overall, the data indicates that we may have discovered a new targeted treatment for MLL rearranged leukemia, which shows excellent clinical properties. We have successfully generated Patient Derived Xenografts (PDX) models and we are currently testing this drug to verify its effectiveness in the treatment on PDX. We will include this data in our presentation. Disclosures No relevant conflicts of interest to declare.

scholarly journals Higher Acid-Base Imbalance Associated with Respiratory Failure Could Decrease the Survival of Patients with Scrub Typhus during Intensive Care Unit Stay: A Gene Set Enrichment Analysis

2019 ◽  
Vol 8 (10) ◽  
pp. 1580 ◽  
Author(s):  
Kyoung Min Moon ◽  
Kyueng-Whan Min ◽  
Mi-Hye Kim ◽  
Dong-Hoon Kim ◽  
Byoung Kwan Son ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Respiratory Failure ◽  
Scrub Typhus ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Acid Base ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Gene Sets

Ninety percent of patients with scrub typhus (SC) with vasculitis-like syndrome recover after mild symptoms; however, 10% can suffer serious complications, such as acute respiratory failure (ARF) and admission to the intensive care unit (ICU). Predictors for the progression of SC have not yet been established, and conventional scoring systems for ICU patients are insufficient to predict severity. We aimed to identify simple and robust indicators to predict aggressive behaviors of SC. We evaluated 91 patients with SC and 81 non-SC patients who were admitted to the ICU, and 32 cases from the public functional genomics data repository for gene expression analysis. We analyzed the relationships between several predictors and clinicopathological characteristics in patients with SC. We performed gene set enrichment analysis (GSEA) to identify SC-specific gene sets. The acid-base imbalance (ABI), measured 24 h before serious complications, was higher in patients with SC than in non-SC patients. A high ABI was associated with an increased incidence of ARF, leading to mechanical ventilation and worse survival. GSEA revealed that SC correlated to gene sets reflecting inflammation/apoptotic response and airway inflammation. ABI can be used to indicate ARF in patients with SC and assist with early detection.

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