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Epigenetic Regulatory Network during Embryonic Development Revealed by Single-Cell Sequencing
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Epigenetic Regulatory Network during Embryonic Development Revealed by Single-Cell Sequencing

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Epigenomics".

Deadline for manuscript submissions: closed (15 January 2024) | Viewed by 2879

Special Issue Editors

Dr. Yun Gao

E-Mail Website
Guest Editor
Department of Chemistry, University of Chicago, 929 E 57th St, Chicago, IL 60637, USA
Interests: single-cell sequencing; epigenetics; embryo development
Dr. Rui Wang

E-Mail Website
Guest Editor
Stanford Cancer Center, Stanford University, Palo Alto, CA, USA
Interests: cancer biology; human embryo development; cell free DNA; single cell sequencing; bioinformatics

Special Issue Information

Dear Colleagues,

During embryonic development, from fertilization to birth, intricate reprogramming occurs, including the transition from totipotency to pluripotency, embryonic layer differentiation, and organogenesis. Interruptions to this tightly regulated process, caused by genetic or maternal environmental factors, result in severe consequences such as failed implantation, organ malformation, and halted development. Understanding the molecular mechanisms of embryonic development is crucial for prenatal diagnosis, ensuring healthy births, and species preservation.

Investigations of the regulatory networks governing the intricate process of embryonic development have been enhanced recently through the use of cutting-edge methodologies. Single-cell RNA sequencing characterizes cell identities, while single-cell ATAC-seq and ChIP-seq identify regulatory elements. In vitro 3D culture systems reveal lineage differentiation, while lineage tracing and spatial omics provide temporal and spatial information during the course of differentiation.

In light of these advancements, the journal Genes is pleased to announce the establishment of a Special Issue titled "Epigenetic Regulatory Network during Embryonic Development Revealed by Single-Cell Sequencing". The primary objective of this Special Issue is to present novel molecular mechanisms underlying embryonic development, state-of-the-art methodologies in epigenetic sequencing, and innovative formulations of in vitro embryonic culture systems. Authors are encouraged to submit various types of contributions, including original research articles, reviews, and reports.

Dr. Yun Gao
Dr. Rui Wang
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. Genes 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

  • epigenetics
  • embryonic development
  • regulatory network
  • organogenesis
  • in vitro 3D culture

Published Papers (1 paper)

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Review

15 pages, 578 KiB  
Review
Healthy Live Births after the Transfer of Mosaic Embryos: Self-Correction or PGT-A Overestimation?
by Gerard Campos, Romualdo Sciorio and Steven Fleming
Genes 2024, 15(1), 18; https://doi.org/10.3390/genes15010018 - 21 Dec 2023
Cited by 1 | Viewed by 2622
Abstract
The implementation of next generation sequencing (NGS) in preimplantation genetic testing for aneuploidy (PGT-A) has led to a higher prevalence of mosaic diagnosis within the trophectoderm (TE) sample. Regardless, mosaicism could potentially increase the rate of live-born children with chromosomic syndromes, though available [...] Read more.
The implementation of next generation sequencing (NGS) in preimplantation genetic testing for aneuploidy (PGT-A) has led to a higher prevalence of mosaic diagnosis within the trophectoderm (TE) sample. Regardless, mosaicism could potentially increase the rate of live-born children with chromosomic syndromes, though available data from the transfer of embryos with putative PGT-A mosaicism are scarce but reassuring. Even with lower implantation and higher miscarriage rates, mosaic embryos can develop into healthy live births. Therefore, this urges an explanation for the disappearance of aneuploid cells throughout development, to provide guidance in the management of mosaicism in clinical practice. Technical overestimation of mosaicism, together with some sort of “self-correction” mechanisms during the early post-implantation stages, emerged as potential explanations. Unlike the animal model, in which the elimination of genetically abnormal cells from the future fetal lineage has been demonstrated, in human embryos this capability remains unverified even though the germ layer displays an aneuploidy-induced cell death lineage preference with higher rates of apoptosis in the inner cell mass (ICM) than in the TE cells. Moreover, the reported differential dynamics of cell proliferation and apoptosis between euploid, mosaic, and aneuploid embryos, together with pro-apoptosis gene products (cfDNA and mRNA) and extracellular vesicles identified in the blastocoel fluid, may support the hypothesis of apoptosis as a mechanism to purge the preimplantation embryo of aneuploid cells. Alternative hypotheses, like correction of aneuploidy by extrusion of a trisomy chromosome or by monosomic chromosome duplication, are even, though they represent an extremely rare phenomenon. On the other hand, the technical limitations of PGT-A analysis may lead to inaccuracy in embryo diagnoses, identifying as “mosaic” those embryos that are uniformly euploid or aneuploid. NGS assumption of “intermediate copy number profiles” as evidence of a mixture of euploid and aneuploid cells in a single biopsy has been reported to be poorly predictive in cases of mosaicism diagnosis. Additionally, the concordance found between the TE and the ICM in cases of TE biopsies displaying mosaicism is lower than expected, and it correlates differently depending on the type (whole chromosome versus segmental) and the level of mosaicism reported. Thus, in cases of low-/medium-level mosaicism (<50%), aneuploid cells would rarely involve the ICM and other regions. However, in high-level mosaics (≥50%), abnormal cells in the ICM should display higher prevalence, revealing more uniform aneuploidy in most embryos, representing a technical variation in the uniform aneuploidy range, and therefore might impair the live birth rate. Full article
(This article belongs to the Special Issue Epigenetic Regulatory Network during Embryonic Development Revealed by Single-Cell Sequencing)
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