Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.8
5.6
Journals
IJMS
Special Issues
Epigenomics of Complex Traits and Diseases 2.0
ijms-logo
Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Epigenomics of Complex Traits and Diseases 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 10533

Special Issue Editor

Dr. Davide Gentilini

E-Mail Website1 Website2
Guest Editor
1. IRCCS Istituto Auxologico Italiano, Milan, Italy
2. Department of Brain and Behavioural Science, University of Pavia, Pavia, Italy
Interests: genomics; epigenetics; statistics; genetic epidemiology; medical statistics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genome-wide genetic information for human populations and phenotypes is becoming increasingly abundant because of the efforts of genomes sequencing projects and the recent wave of genome-wide association studies (GWASs) in human complex traits. Thousands of genetic variants have been associated with diseases and complex traits, with very good estimates of the effect size and the significance of the effects. While this is a major milestone in human genetics, these studies generally failed in their primary intent. Despite the hundreds of millions of dollars spent on genome-wide association studies, most of the genetic variance in the risks for the most common diseases remains undiscovered. Recent advances in genomic technologies have placed us in a position to initiate large-scale studies of human disease-associated epigenetic variation, specifically variations in DNA methylation. Epigenetics appears to be an interesting opportunity to shed light on the genomic contribution in the field of complex traits and diseases.

Topics of this Special Issue include, but are not limited to, the following:

  • Genetic and epigenetic variability of complex traits and diseases
  • Genetics and epigenetics of aging
  • Epigenetics modification in cancer
  • Epigenomic-wide association studies in the field of complex traits and diseases
  • Methodological approaches for the integration of omic data

Dr. Davide Gentilini
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.

Published Papers (4 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

10 pages, 1230 KiB  
Article
Experiences of Trauma and DNA Methylation Profiles among African American Mothers and Children
by Veronica Barcelona, Yunfeng Huang, Billy A. Caceres, Kevin P. Newhall, Qin Hui, Jessica P. Cerdeña, Cindy A. Crusto, Yan V. Sun and Jacquelyn Y. Taylor
Int. J. Mol. Sci. 2022, 23(16), 8951; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23168951 - 11 Aug 2022
Cited by 2 | Viewed by 2105
Abstract
Potentially traumatic experiences have been associated with chronic diseases. Epigenetic mechanisms, including DNA methylation (DNAm), have been proposed as an explanation for this association. We examined the association of experiences of trauma with epigenome-wide DNAm among African American mothers (n = 236) [...] Read more.
Potentially traumatic experiences have been associated with chronic diseases. Epigenetic mechanisms, including DNA methylation (DNAm), have been proposed as an explanation for this association. We examined the association of experiences of trauma with epigenome-wide DNAm among African American mothers (n = 236) and their children aged 3–5 years (n = 232; N = 500), using the Life Events Checklist-5 (LEC) and Traumatic Events Screening Inventory—Parent Report Revised (TESI-PRR). We identified no DNAm sites significantly associated with potentially traumatic experience scores in mothers. One CpG site on the ENOX1 gene was methylome-wide-significant in children (FDR-corrected q-value = 0.05) from the TESI-PRR. This protein-coding gene is associated with mental illness, including unipolar depression, bipolar, and schizophrenia. Future research should further examine the associations between childhood trauma, DNAm, and health outcomes among this understudied and high-risk group. Findings from such longitudinal research may inform clinical and translational approaches to prevent adverse health outcomes associated with epigenetic changes. Full article
(This article belongs to the Special Issue Epigenomics of Complex Traits and Diseases 2.0)
►▼ Show Figures

Figure 1

14 pages, 3857 KiB  
Article
High-Throughput Screen Detects Calcium Signaling Dysfunction in Hutchinson-Gilford Progeria Syndrome
by Juan A. Fafián-Labora, Miriam Morente-López, Fco. Javier de Toro and María C. Arufe
Int. J. Mol. Sci. 2021, 22(14), 7327; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22147327 - 07 Jul 2021
Cited by 4 | Viewed by 2533
Abstract
Hutchinson–Gilford progeria syndrome (HGPS) is a deadly childhood disorder, which is considered a very rare disease. It is caused by an autosomal dominant mutation on the LMNA gene, and it is characterized by accelerated aging. Human cell lines from HGPS patients and healthy [...] Read more.
Hutchinson–Gilford progeria syndrome (HGPS) is a deadly childhood disorder, which is considered a very rare disease. It is caused by an autosomal dominant mutation on the LMNA gene, and it is characterized by accelerated aging. Human cell lines from HGPS patients and healthy parental controls were studied in parallel using next-generation sequencing (NGS) to unravel new non-previously altered molecular pathways. Nine hundred and eleven transcripts were differentially expressed when comparing healthy versus HGPS cell lines from a total of 21,872 transcripts; ITPR1, ITPR3, CACNA2D1, and CAMK2N1 stood out among them due to their links with calcium signaling, and these were validated by Western blot analysis. It was observed that the basal concentration of intracellular Ca2+ was statistically higher in HGPS cell lines compared to healthy ones. The relationship between genes involved in Ca2+ signaling and mitochondria-associated membranes (MAM) was demonstrated through cytosolic calcium handling by means of an automated fluorescent plate reading system (FlexStation 3, Molecular Devices), and apoptosis and mitochondrial ROS production were examined by means of flow cytometry analysis. Altogether, our data suggest that the Ca2+ signaling pathway is altered in HGPS at least in part due to the overproduction of reactive oxygen species (ROS). Our results unravel a new therapeutic window for the treatment of this rare disease and open new strategies to study pathologies involving both accelerated and healthy aging. Full article
(This article belongs to the Special Issue Epigenomics of Complex Traits and Diseases 2.0)
►▼ Show Figures

Figure 1

18 pages, 3682 KiB  
Article
Immunomodulatory Effects of Vitamin D Supplementation in a Deficient Population
by Mathieu Garand, Mohammed Toufiq, Parul Singh, Susie Shih Yin Huang, Sara Tomei, Rebecca Mathew, Valentina Mattei, Mariam Al Wakeel, Elham Sharif and Souhaila Al Khodor
Int. J. Mol. Sci. 2021, 22(9), 5041; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22095041 - 10 May 2021
Cited by 7 | Viewed by 3280
Abstract
In addition to its canonical functions, vitamin D has been proposed to be an important mediator of the immune system. Despite ample sunshine, vitamin D deficiency is prevalent (>80%) in the Middle East, resulting in a high rate of supplementation. However, the underlying [...] Read more.
In addition to its canonical functions, vitamin D has been proposed to be an important mediator of the immune system. Despite ample sunshine, vitamin D deficiency is prevalent (>80%) in the Middle East, resulting in a high rate of supplementation. However, the underlying molecular mechanisms of the specific regimen prescribed and the potential factors affecting an individual’s response to vitamin D supplementation are not well characterized. Our objective is to describe the changes in the blood transcriptome and explore the potential mechanisms associated with vitamin D3 supplementation in one hundred vitamin D-deficient women who were given a weekly oral dose (50,000 IU) of vitamin D3 for three months. A high-throughput targeted PCR, composed of 264 genes representing the important blood transcriptomic fingerprints of health and disease states, was performed on pre and post-supplementation blood samples to profile the molecular response to vitamin D3. We identified 54 differentially expressed genes that were strongly modulated by vitamin D3 supplementation. Network analyses showed significant changes in the immune-related pathways such as TLR4/CD14 and IFN receptors, and catabolic processes related to NF-kB, which were subsequently confirmed by gene ontology enrichment analyses. We proposed a model for vitamin D3 response based on the expression changes of molecules involved in the receptor-mediated intra-cellular signaling pathways and the ensuing predicted effects on cytokine production. Overall, vitamin D3 has a strong effect on the immune system, G-coupled protein receptor signaling, and the ubiquitin system. We highlighted the major molecular changes and biological processes induced by vitamin D3, which will help to further investigate the effectiveness of vitamin D3 supplementation among individuals in the Middle East as well as other regions. Full article
(This article belongs to the Special Issue Epigenomics of Complex Traits and Diseases 2.0)
►▼ Show Figures

Figure 1

Review

Jump to: Research

19 pages, 1133 KiB  
Review
Non-Coding RNAs in Pulmonary Diseases: Comparison of Different Airway-Derived Biosamples
by Zuzanna Stachowiak, Beata Narożna and Aleksandra Szczepankiewicz
Int. J. Mol. Sci. 2023, 24(3), 2006; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24032006 - 19 Jan 2023
Cited by 5 | Viewed by 1754
Abstract
Due to their structural conservation and functional role in critical signalling pathways, non-coding RNA (ncRNA) is a promising biomarker and modulator of pathological conditions. Most research has focussed on the role of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These [...] Read more.
Due to their structural conservation and functional role in critical signalling pathways, non-coding RNA (ncRNA) is a promising biomarker and modulator of pathological conditions. Most research has focussed on the role of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These molecules have been investigated both in a cellular and an extracellular context. Sources of ncRNAs may include organ-specific body fluids. Therefore, studies on ncRNAs in respiratory diseases include those on sputum, bronchoalveolar lavage fluid (BALF) and exhaled breath condensate (EBC). It is worth identifying the limitations of these biosamples in terms of ncRNA abundance, processing and diagnostic potential. This review describes the progress in the literature on the role of ncRNAs in the pathogenesis and progression of severe respiratory diseases, including cystic fibrosis, asthma and interstitial lung disease. We showed that there is a deficit of information on lncRNAs and circRNAs in selected diseases, despite attempts to functionally bind them to miRNAs. miRNAs remain the most well-studied, but only a few investigations have been conducted on the least invasive biosample material, i.e., EBC. To summarise the studies conducted to date, we also performed a preliminary in silico analysis of the reported miRNAs, demonstrating the complexity of their role and interactions in selected respiratory diseases. Full article
(This article belongs to the Special Issue Epigenomics of Complex Traits and Diseases 2.0)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop