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Life
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Genomics and Epigenomics of Human Complex Diseases
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Genomics and Epigenomics of Human Complex Diseases

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: closed (21 May 2021) | Viewed by 15701

Special Issue Editors

Dr. Nora Fernandez-Jimenez

E-Mail Website
Guest Editor
1. Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, 48940 Leioa, Spain
2. Biocruces-Bizkaia Health Research Institute, 48903 Barakaldo, Spain
Interests: genomics; epigenomics; DNA methylation; complex diseases; celiac disease; gene expression; childhood development
Dr. Iraia Garcia-Santisteban

E-Mail Website
Guest Editor
Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, 48940 Leioa, Spain and Biocruces-Bizkaia Health Research Institute, 48903 Barakaldo, Spain
Interests: genomics, epigenomics and transcriptomics; immune-related diseases; cell cycle; DNA damage; deubiquitinases

Special Issue Information

Dear Colleagues,

The knowledge on genomics has widened enormously in the last decade, enabling a better understanding of human diseases. Besides, epigenomics has emerged as the bridge between the environment and the genome, and is being studied in different contexts, including a variety of traits, cell types, tissues and environmental conditions. Additionally, we are witnessing an explosion of analytical methods that allow us to interweave and integrate OMICs data and thus rediscover how (epi)genomic layers interact with each other and with complex phenotypes. This progress, possible only through technological and analytical advances, is contributing to the search for diagnostic markers, tailored interventions and preventive approaches applicable to clinical settings in the context of human complex diseases.

This Special Issue will provide readers with cutting-edge knowledge on “Genomics and Epigenomics of Human Complex Diseases”. In particular, we aim to collect original research papers and reviews on the genomic and epigenomic profiling of complex conditions, and we will especially welcome studies integrating different OMICs and trying to go beyond traditional analytical pipelines. In this sense, purely bioinformatics work and innovative reanalysis and reinterpretation of published data will also be considered for publication, with particular emphasis on papers describing translational application to the clinic. Therefore, this collection of interdisciplinary papers about Genomics and Epigenomics of Human Complex Diseases will be a good reference for a broad range of readers, including geneticists, medical doctors, bench biologists, data analysts and genetic epidemiologists.

Dr. Nora Fernandez-Jimenez
Dr. Iraia Garcia-Santisteban
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. Life 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

  • GWAS
  • QTLs
  • transcriptomics
  • DNA methylation
  • chromatin modifications
  • epitranscriptomics
  • coexpression networks
  • (Epi)genomic data analysis
  • mendelian randomization
  • medical statistics and methods
  • bioinformatics

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

Published Papers (3 papers)

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Research

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12 pages, 1809 KiB  
Article
Transcription Factor Activity Inference in Systemic Lupus Erythematosus
by Raul Lopez-Dominguez, Daniel Toro-Dominguez, Jordi Martorell-Marugan, Adrian Garcia-Moreno, Christian H. Holland, Julio Saez-Rodriguez, Daniel Goldman, Michelle A. Petri, Marta E. Alarcon-Riquelme and Pedro Carmona-Saez
Life 2021, 11(4), 299; https://doi.org/10.3390/life11040299 - 1 Apr 2021
Cited by 8 | Viewed by 4332
Abstract
Background: Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disease with diverse clinical manifestations. Although most of the SLE-associated loci are located in regulatory regions, there is a lack of global information about transcription factor (TFs) activities, the mode of regulation of the [...] Read more.
Background: Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disease with diverse clinical manifestations. Although most of the SLE-associated loci are located in regulatory regions, there is a lack of global information about transcription factor (TFs) activities, the mode of regulation of the TFs, or the cell or sample-specific regulatory circuits. The aim of this work is to decipher TFs implicated in SLE. Methods: In order to decipher regulatory mechanisms in SLE, we have inferred TF activities from transcriptomic data for almost all human TFs, defined clusters of SLE patients based on the estimated TF activities and analyzed the differential activity patterns among SLE and healthy samples in two different cohorts. The Transcription Factor activity matrix was used to stratify SLE patients and define sets of TFs with statistically significant differential activity among the disease and control samples. Results: TF activities were able to identify two main subgroups of patients characterized by distinct neutrophil-to-lymphocyte ratio (NLR), with consistent patterns in two independent datasets—one from pediatric patients and other from adults. Furthermore, after contrasting all subgroups of patients and controls, we obtained a significant and robust list of 14 TFs implicated in the dysregulation of SLE by different mechanisms and pathways. Among them, well-known regulators of SLE, such as STAT or IRF, were found, but others suggest new pathways that might have important roles in SLE. Conclusions: These results provide a foundation to comprehend the regulatory mechanism underlying SLE and the established regulatory factors behind SLE heterogeneity that could be potential therapeutic targets. Full article
(This article belongs to the Special Issue Genomics and Epigenomics of Human Complex Diseases)
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12 pages, 1305 KiB  
Article
A Systematic Two-Sample Mendelian Randomization Analysis Identifies Shared Genetic Origin of Endometriosis and Associated Phenotypes
by Aiara Garitazelaia, Aintzane Rueda-Martínez, Rebeca Arauzo, Jokin de Miguel, Ariadna Cilleros-Portet, Sergi Marí, Jose Ramon Bilbao, Nora Fernandez-Jimenez and Iraia García-Santisteban
Life 2021, 11(1), 24; https://doi.org/10.3390/life11010024 - 3 Jan 2021
Cited by 16 | Viewed by 4790
Abstract
Endometriosis, one of the most common gynecological disorders, is a complex disease characterized by the growth of endometrial-like tissue in extra-uterine locations and is a cause of pelvic pain and infertility. Evidence from observational studies indicate that endometriosis usually appears together with several [...] Read more.
Endometriosis, one of the most common gynecological disorders, is a complex disease characterized by the growth of endometrial-like tissue in extra-uterine locations and is a cause of pelvic pain and infertility. Evidence from observational studies indicate that endometriosis usually appears together with several other phenotypes. These include a list of autoimmune diseases, most of them more prevalent in women, anthropometric traits associated with leanness in the adulthood, as well as female reproductive traits, including altered hormone levels and those associated with a prolonged exposure to menstruation. However, the biological mechanisms underlying their co-morbidity remains unknown. To explore whether those phenotypes and endometriosis share a common genetic origin, we performed a systematic Two-Sample Mendelian Randomization (2SMR) analysis using public GWAS data. Our results suggest potential common genetic roots between endometriosis and female anthropometric and reproductive traits. Particularly, our data suggests that reduced weight and BMI might be mediating the genetic susceptibility to suffer endometriosis. Furthermore, data on female reproductive traits strongly suggest that genetic variants that predispose to a more frequent exposure to menstruation, through earlier age at menarche and shorter menstrual cycles, might also increase the risk to suffer from endometriosis. Full article
(This article belongs to the Special Issue Genomics and Epigenomics of Human Complex Diseases)
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Review

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16 pages, 1085 KiB  
Review
Alteration of Genomic Imprinting after Assisted Reproductive Technologies and Long-Term Health
by Eguzkine Ochoa
Life 2021, 11(8), 728; https://doi.org/10.3390/life11080728 - 22 Jul 2021
Cited by 6 | Viewed by 5416
Abstract
Assisted reproductive technologies (ART) are the treatment of choice for some infertile couples and even though these procedures are generally considered safe, children conceived by ART have shown higher reported risks of some perinatal and postnatal complications such as low birth weight, preterm [...] Read more.
Assisted reproductive technologies (ART) are the treatment of choice for some infertile couples and even though these procedures are generally considered safe, children conceived by ART have shown higher reported risks of some perinatal and postnatal complications such as low birth weight, preterm birth, and childhood cancer. In addition, the frequency of some congenital imprinting disorders, like Beckwith–Wiedemann Syndrome and Silver–Russell Syndrome, is higher than expected in the general population after ART. Experimental evidence from animal studies suggests that ART can induce stress in the embryo and influence gene expression and DNA methylation. Human epigenome studies have generally revealed an enrichment of alterations in imprinted regions in children conceived by ART, but no global methylation alterations. ART procedures occur simultaneously with the establishment and maintenance of imprinting during embryonic development, so this may underlie the apparent sensitivity of imprinted regions to ART. The impact in adulthood of imprinting alterations that occurred during early embryonic development is still unclear, but some experimental evidence in mice showed higher risk to obesity and cardiovascular disease after the restriction of some imprinted genes in early embryonic development. This supports the hypothesis that imprinting alterations in early development might induce epigenetic programming of metabolism and affect long-term health. Given the growing use of ART, it is important to determine the impact of ART in genomic imprinting and long-term health. Full article
(This article belongs to the Special Issue Genomics and Epigenomics of Human Complex Diseases)
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