Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.2
3.9
Journals
Biomedicines
Special Issues
Genome-Environment Interactions in Psychiatric Disorders and Neurodegenerative Diseases
share announcement

Genome-Environment Interactions in Psychiatric Disorders and Neurodegenerative Diseases

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Cell Biology and Pathology".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 19841

Special Issue Editors

Dr. Roberto Carlos Agis-Balboa

E-Mail Website
Guest Editor
1. NeuroEpigenetics Lab, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
2. Grupo Trastornos del Movimiento, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain
3. Translational Neuroscience Group-CIBERSAM, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, 36213 Vigo, Spain
Interests: epigenetics; neuropsychiatric diseases (e.g., depression, schizophrenia, PTSD, Alzheimer’s); biomarkers; therapeutic targets; bioinformatic tools; psychiatry; artificial intelligence and neuroscience
Dr. Hugo Lopez-Fernandez

E-Mail Website
Guest Editor
1. CINBIO, Department of Computer Science, ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain
2. SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
Interests: scientific software applications; data analysis (R, Python); automated analysis pipelines; machine learning; bioinformatics (genomics, proteomics, etc.); medical informatics (e.g., application of deep learning for medical image analysis)

Special Issue Information

Dear Colleagues,

Some psychiatric disorders (e.g., schizophrenia, depression, bipolar disorder, posttraumatic stress disorder) and neurodegenerative diseases (Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, etc.) represent serious problems in today’s society. The genome-environment interactions occurring in these diseases are currently one of the hottest topics in neuroscience research. They are of great clinical importance, but still poorly understood. The combination of conventional molecular techniques with more advanced tools (omics, artificial intelligence, etc.) is accelerating advances in basic and clinical research. Altogether this will help us to find biomarkers; to decipher the “epigenetic signature”; and to design strategies to prevent, diagnose, and treat these devastating diseases.

The objective of this Special Issue of Biomedicines is to bring together worldwide experts that provide an integral overview and discuss the latest advances in the field of genome-environment interactions associated with both psychiatric disorders and neurodegenerative diseases.

Contributions are welcome in the form of original research and review articles.

Dr. Roberto Carlos Agis-Balboa
Dr. Hugo Lopez-Fernandez
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • epigenetic mechanisms
  • DNA methylation
  • miRNAs
  • histone acetylation
  • neurodegenerative diseases
  • psychiatric disorders
  • epigenetic signature
  • genome-wide environmental interaction (GWEI) studies
  • bioinformatics
  • artificial intelligence
  • omics

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (7 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review, Other

15 pages, 2869 KiB  
Article
MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders
by Daniel Pérez-Rodríguez, Roberto Carlos Agís-Balboa and Hugo López-Fernández
Biomedicines 2023, 11(4), 1230; https://doi.org/10.3390/biomedicines11041230 - 21 Apr 2023
Cited by 2 | Viewed by 3474
Abstract
High-throughput sequencing of small RNA molecules such as microRNAs (miRNAs) has become a widely used approach for studying gene expression and regulation. However, analyzing miRNA-Seq data can be challenging because it requires multiple steps, from quality control and preprocessing to differential expression and [...] Read more.
High-throughput sequencing of small RNA molecules such as microRNAs (miRNAs) has become a widely used approach for studying gene expression and regulation. However, analyzing miRNA-Seq data can be challenging because it requires multiple steps, from quality control and preprocessing to differential expression and pathway-enrichment analyses, with many tools and databases available for each step. Furthermore, reproducibility of the analysis pipeline is crucial to ensure that the results are accurate and reliable. Here, we present myBrain-Seq, a comprehensive and reproducible pipeline for analyzing miRNA-Seq data that incorporates miRNA-specific solutions at each step of the analysis. The pipeline was designed to be flexible and user-friendly, allowing researchers with different levels of expertise to perform the analysis in a standardized and reproducible manner, using the most common and widely used tools for each step. In this work, we describe the implementation of myBrain-Seq and demonstrate its capacity to consistently and reproducibly identify differentially expressed miRNAs and enriched pathways by applying it to a real case study in which we compared schizophrenia patients who responded to medication with treatment-resistant schizophrenia patients to obtain a 16-miRNA treatment-resistant schizophrenia profile. Full article
(This article belongs to the Special Issue Genome-Environment Interactions in Psychiatric Disorders and Neurodegenerative Diseases)
►▼ Show Figures

Figure 1

17 pages, 3495 KiB  
Article
Neuroinflammation, Energy and Sphingolipid Metabolism Biomarkers Are Revealed by Metabolic Modeling of Autistic Brains
by Elif Esvap and Kutlu O. Ulgen
Biomedicines 2023, 11(2), 583; https://doi.org/10.3390/biomedicines11020583 - 16 Feb 2023
Cited by 5 | Viewed by 2456
Abstract
Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders generally characterized by repetitive behaviors and difficulties in communication and social behavior. Despite its heterogeneous nature, several metabolic dysregulations are prevalent in individuals with ASD. This work aims to understand ASD brain [...] Read more.
Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders generally characterized by repetitive behaviors and difficulties in communication and social behavior. Despite its heterogeneous nature, several metabolic dysregulations are prevalent in individuals with ASD. This work aims to understand ASD brain metabolism by constructing an ASD-specific prefrontal cortex genome-scale metabolic model (GEM) using transcriptomics data to decipher novel neuroinflammatory biomarkers. The healthy and ASD-specific models are compared via uniform sampling to identify ASD-exclusive metabolic features. Noticeably, the results of our simulations and those found in the literature are comparable, supporting the accuracy of our reconstructed ASD model. We identified that several oxidative stress, mitochondrial dysfunction, and inflammatory markers are elevated in ASD. While oxidative phosphorylation fluxes were similar for healthy and ASD-specific models, and the fluxes through the pathway were nearly undisturbed, the tricarboxylic acid (TCA) fluxes indicated disruptions in the pathway. Similarly, the secretions of mitochondrial dysfunction markers such as pyruvate are found to be higher, as well as the activities of oxidative stress marker enzymes like alanine and aspartate aminotransferases (ALT and AST) and glutathione-disulfide reductase (GSR). We also detected abnormalities in the sphingolipid metabolism, which has been implicated in many inflammatory and immune processes, but its relationship with ASD has not been thoroughly explored in the existing literature. We suggest that important sphingolipid metabolites, such as sphingosine-1-phosphate (S1P), ceramide, and glucosylceramide, may be promising biomarkers for the diagnosis of ASD and provide an opportunity for the adoption of early intervention for young children. Full article
(This article belongs to the Special Issue Genome-Environment Interactions in Psychiatric Disorders and Neurodegenerative Diseases)
►▼ Show Figures

Graphical abstract

20 pages, 4327 KiB  
Article
Data-Driven Phenotyping of Alzheimer’s Disease under Epigenetic Conditions Using Partial Volume Correction of PET Studies and Manifold Learning
by Silvia Campanioni, José A. González-Nóvoa, Laura Busto, Roberto Carlos Agís-Balboa and César Veiga
Biomedicines 2023, 11(2), 273; https://doi.org/10.3390/biomedicines11020273 - 19 Jan 2023
Cited by 1 | Viewed by 1863
Abstract
Alzheimer’s disease (AD) is the most common form of dementia. An increasing number of studies have confirmed epigenetic changes in AD. Consequently, a robust phenotyping mechanism must take into consideration the environmental effects on the patient in the generation of phenotypes. Positron Emission [...] Read more.
Alzheimer’s disease (AD) is the most common form of dementia. An increasing number of studies have confirmed epigenetic changes in AD. Consequently, a robust phenotyping mechanism must take into consideration the environmental effects on the patient in the generation of phenotypes. Positron Emission Tomography (PET) is employed for the quantification of pathological amyloid deposition in brain tissues. The objective is to develop a new methodology for the hyperparametric analysis of changes in cognitive scores and PET features to test for there being multiple AD phenotypes. We used a computational method to identify phenotypes in a retrospective cohort study (532 subjects), using PET and Magnetic Resonance Imaging (MRI) images and neuropsychological assessments, to develop a novel computational phenotyping method that uses Partial Volume Correction (PVC) and subsets of neuropsychological assessments in a non-biased fashion. Our pipeline is based on a Regional Spread Function (RSF) method for PVC and a t-distributed Stochastic Neighbor Embedding (t-SNE) manifold. The results presented demonstrate that (1) the approach to data-driven phenotyping is valid, (2) the different techniques involved in the pipelines produce different results, and (3) they permit us to identify the best phenotyping pipeline. The method identifies three phenotypes and permits us to analyze them under epigenetic conditions. Full article
(This article belongs to the Special Issue Genome-Environment Interactions in Psychiatric Disorders and Neurodegenerative Diseases)
►▼ Show Figures

Figure 1

15 pages, 1935 KiB  
Article
L-Serine Influences Epigenetic Modifications to Improve Cognition and Behaviors in Growth Hormone-Releasing Hormone Knockout Mice
by Fang Zhang, Mert Icyuz, Trygve Tollefsbol, Paul Alan Cox, Sandra Anne Banack and Liou Y. Sun
Biomedicines 2023, 11(1), 104; https://doi.org/10.3390/biomedicines11010104 - 30 Dec 2022
Cited by 3 | Viewed by 2655
Abstract
Neurodegenerative diseases feature changes in cognition, and anxiety-like and autism-like behaviors, which are associated with epigenetic alterations such as DNA methylation and histone modifications. The amino acid L-serine has been shown to have beneficial effects on neurological symptoms. Here, we found that growth [...] Read more.
Neurodegenerative diseases feature changes in cognition, and anxiety-like and autism-like behaviors, which are associated with epigenetic alterations such as DNA methylation and histone modifications. The amino acid L-serine has been shown to have beneficial effects on neurological symptoms. Here, we found that growth hormone-releasing hormone knockout (GHRH-KO) mice, a GH-deficiency mouse model characterized by extended lifespan and enhanced insulin sensitivity, showed a lower anxiety symptom and impairment of short-term object recognition memory and autism-like behaviors. Interestingly, L-serine administration exerted anxiolytic effects in mice and ameliorated the behavioral deficits in GHRH-KO. L-serine treatment upregulated histone epigenetic markers of H3K4me, H3K9ac, H3K14ac and H3K18ac in the hippocampus and H3K4me in the cerebral cortex in both GHRH-KO mice and wild type controls. L-serine-modulated epigenetic marker changes, in turn, were found to regulate mRNA expression of BDNF, grm3, foxp1, shank3, auts2 and marcksl1, which are involved in anxiety-, cognitive- and autism-like behaviors. Our study provides a novel insight into the beneficial effects of L-serine intervention on neuropsychological impairments. Full article
(This article belongs to the Special Issue Genome-Environment Interactions in Psychiatric Disorders and Neurodegenerative Diseases)
►▼ Show Figures

Figure 1

15 pages, 3341 KiB  
Article
APOE ε4 in Depression-Associated Memory Impairment—Evidence from Genetic and MicroRNA Analyses
by Sarah Bonk, Kevin Kirchner, Sabine Ameling, Linda Garvert, Henry Völzke, Matthias Nauck, Uwe Völker, Hans J. Grabe and Sandra Van der Auwera
Biomedicines 2022, 10(7), 1560; https://doi.org/10.3390/biomedicines10071560 - 30 Jun 2022
Cited by 7 | Viewed by 2503
Abstract
(1) Background: The aim of this study was to replicate a reported interaction between APOE ε4 status and depression on memory function in two independent, nondemented samples from the general population and to examine the potential role of circulating plasma miRNAs. (2) Methods: [...] Read more.
(1) Background: The aim of this study was to replicate a reported interaction between APOE ε4 status and depression on memory function in two independent, nondemented samples from the general population and to examine the potential role of circulating plasma miRNAs. (2) Methods: The impact of the APOE ε4 allele on verbal memory and the interaction with depression is investigated in two large general-population cohorts from the Study of Health in Pomerania (SHIP, total n = 6286). Additionally, biological insights are gained by examining the potential role of circulating plasma miRNAs as potential epigenetic regulators. Analyses are performed using linear regression models adjusted for relevant biological and environmental covariates. (3) Results: Current depression as well as carrying the APOE ε4 allele were associated with impaired memory performance, with increasing effect for subjects with both risk factors. In a subcohort with available miRNA data subjects with current depressive symptoms and carrying APOE e4 revealed reduced levels of hsa-miR-107, a prominent risk marker for early Alzheimer’s Disease. (4) Conclusions: Our results confirm the effect of depressive symptoms and APOE ε4 status on memory performance. Additionally, miRNA analysis identified hsa-miR-107 as a possible biological link between APOE ε4, depressive symptoms, and cognitive impairment. Full article
(This article belongs to the Special Issue Genome-Environment Interactions in Psychiatric Disorders and Neurodegenerative Diseases)
►▼ Show Figures

Figure 1

Review

Jump to: Research, Other

14 pages, 592 KiB  
Review
Genome–Environment Interactions and Psychiatric Disorders
by Jacob Peedicayil
Biomedicines 2023, 11(4), 1209; https://doi.org/10.3390/biomedicines11041209 - 19 Apr 2023
Cited by 5 | Viewed by 3610
Abstract
Environmental factors are known to interact with the genome by altering epigenetic mechanisms regulating gene expression and contributing to the pathogenesis of psychiatric disorders. This article is a narrative review of how the major environmental factors contribute to the pathogenesis of common psychiatric [...] Read more.
Environmental factors are known to interact with the genome by altering epigenetic mechanisms regulating gene expression and contributing to the pathogenesis of psychiatric disorders. This article is a narrative review of how the major environmental factors contribute to the pathogenesis of common psychiatric disorders such as schizophrenia, bipolar disorder, major depressive disorder, and anxiety disorder this way. The cited articles were published between 1 January 2000 and 31 December 2022 and were obtained from PubMed and Google Scholar. The search terms used were as follows: gene or genetic; genome; environment; mental or psychiatric disorder; epigenetic; and interaction. The following environmental factors were found to act epigenetically on the genome to influence the pathogenesis of psychiatric disorders: social determinants of mental health, maternal prenatal psychological stress, poverty, migration, urban dwelling, pregnancy and birth complications, alcohol and substance abuse, microbiota, and prenatal and postnatal infections. The article also discusses the ways by which factors such as drugs, psychotherapy, electroconvulsive therapy, and physical exercise act epigenetically to alleviate the symptoms of psychiatric disorders in affected patients. These data will be useful information for clinical psychiatrists and those researching the pathogenesis and treatment of psychiatric disorders. Full article
(This article belongs to the Special Issue Genome-Environment Interactions in Psychiatric Disorders and Neurodegenerative Diseases)
►▼ Show Figures

Figure 1

Other

Jump to: Research, Review

15 pages, 487 KiB  
Systematic Review
A Scoping Review of Rodent Studies Investigating the Epigenetic Mechanisms in the Brain Underlying the Effects of Diet on Depressive-like Behaviour
by Carla L. Sánchez-Lafuente, Brady S. Reive, Lisa E. Kalynchuk and Hector J. Caruncho
Biomedicines 2022, 10(12), 3213; https://doi.org/10.3390/biomedicines10123213 - 11 Dec 2022
Cited by 1 | Viewed by 1753
Abstract
A healthy diet has been highly associated with a decreased risk for mental health problems such as major depression. Evidence from human studies shows that diet can influence mood but there is a poor understanding of the molecular mechanisms behind these effects, especially [...] Read more.
A healthy diet has been highly associated with a decreased risk for mental health problems such as major depression. Evidence from human studies shows that diet can influence mood but there is a poor understanding of the molecular mechanisms behind these effects, especially the role of epigenetic alterations in the brain. Our objective was to use the Preferred Reporting Items for Systematic Reviews and Meta-Analysis extension for Scoping Reviews (PRISMA-ScR) format to gather all recent studies using animal models that investigate direct or indirect (on the offspring) effects of diet on depressive symptoms, including studies that assess epigenetic mechanisms in the brain. In this format, two authors conducted independent database searches of PubMed, Web of Science, and Academic search premier using one search block “diet epigenetics depression” to find papers published between 2000 and 2022. Relevant studies were selected using pre-defined inclusion/exclusion criteria that were performed independently by the two authors before a subset of studies were selected for qualitative analysis. A total of 11 studies met the inclusion criteria for this systematic scoping review. We found that the literature focuses primarily on the effects of individual nutrients, instead of a specific diet, on despair-like behaviour and anxiety. Studies are heterogenous with the techniques used to asses epigenetic changes in the brain and therefore making it hard to reach common mechanistic explanations. However, all studies report diet-induced changes in the epigenome mainly by the action of DNA methylation, histone acetylation and microRNAs that are parallelel with changes in behaviour. Moreover studies show that inadequate maternal diets can make the offspring more susceptible to develop anxiety and depressive-like behaviour later in life, which is paralleled with changes in the epigenome. Overall, this systematic review shows that there is some literature suggesting a role of brain epigenetics on the diet-induced protective or detrimental effects, specifically on anxiety and depressive-like behaviour. However, studies are limited, lacking the study of some types of diets, behavioural tasks or epigenetic mechanisms. Nevertherless, it shows the importance of genome-environment interactions, bringing new insights towards mechanisms that could be involved in the pathophysiology of mood disorders as well as putative therapeutic targets. Full article
(This article belongs to the Special Issue Genome-Environment Interactions in Psychiatric Disorders and Neurodegenerative Diseases)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-7
Back to TopTop