Cargando…

Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes

Stem cells encompass a variety of different cell types which converge on the dual capacity to self-renew and differentiate into one or more lineages. These characteristic features are key for the involvement of stem cells in crucial biological processes such as development and ageing. To decipher th...

Descripción completa

Detalles Bibliográficos
Autores principales: Barata, Tânia, Duarte, Isabel, Futschik, Matthias E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048104/
https://www.ncbi.nlm.nih.gov/pubmed/36981016
http://dx.doi.org/10.3390/genes14030745
_version_ 1785014096606789632
author Barata, Tânia
Duarte, Isabel
Futschik, Matthias E.
author_facet Barata, Tânia
Duarte, Isabel
Futschik, Matthias E.
author_sort Barata, Tânia
collection PubMed
description Stem cells encompass a variety of different cell types which converge on the dual capacity to self-renew and differentiate into one or more lineages. These characteristic features are key for the involvement of stem cells in crucial biological processes such as development and ageing. To decipher their underlying genetic substrate, it is important to identify so-called stemness genes that are common to different stem cell types and are consistently identified across different studies. In this meta-analysis, 21 individual stemness signatures for humans and another 21 for mice, obtained from a variety of stem cell types and experimental techniques, were compared. Although we observed biological and experimental variability, a highly significant overlap between gene signatures was identified. This enabled us to define integrated stemness signatures (ISSs) comprised of genes frequently occurring among individual stemness signatures. Such integrated signatures help to exclude false positives that can compromise individual studies and can provide a more robust basis for investigation. To gain further insights into the relevance of ISSs, their genes were functionally annotated and connected within a molecular interaction network. Most importantly, the present analysis points to the potential roles of several less well-studied genes in stemness and thus provides promising candidates for further experimental validation.
format Online
Article
Text
id pubmed-10048104
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-100481042023-03-29 Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes Barata, Tânia Duarte, Isabel Futschik, Matthias E. Genes (Basel) Article Stem cells encompass a variety of different cell types which converge on the dual capacity to self-renew and differentiate into one or more lineages. These characteristic features are key for the involvement of stem cells in crucial biological processes such as development and ageing. To decipher their underlying genetic substrate, it is important to identify so-called stemness genes that are common to different stem cell types and are consistently identified across different studies. In this meta-analysis, 21 individual stemness signatures for humans and another 21 for mice, obtained from a variety of stem cell types and experimental techniques, were compared. Although we observed biological and experimental variability, a highly significant overlap between gene signatures was identified. This enabled us to define integrated stemness signatures (ISSs) comprised of genes frequently occurring among individual stemness signatures. Such integrated signatures help to exclude false positives that can compromise individual studies and can provide a more robust basis for investigation. To gain further insights into the relevance of ISSs, their genes were functionally annotated and connected within a molecular interaction network. Most importantly, the present analysis points to the potential roles of several less well-studied genes in stemness and thus provides promising candidates for further experimental validation. MDPI 2023-03-18 /pmc/articles/PMC10048104/ /pubmed/36981016 http://dx.doi.org/10.3390/genes14030745 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Barata, Tânia
Duarte, Isabel
Futschik, Matthias E.
Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes
title Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes
title_full Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes
title_fullStr Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes
title_full_unstemmed Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes
title_short Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes
title_sort integration of stemness gene signatures reveals core functional modules of stem cells and potential novel stemness genes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048104/
https://www.ncbi.nlm.nih.gov/pubmed/36981016
http://dx.doi.org/10.3390/genes14030745
work_keys_str_mv AT baratatania integrationofstemnessgenesignaturesrevealscorefunctionalmodulesofstemcellsandpotentialnovelstemnessgenes
AT duarteisabel integrationofstemnessgenesignaturesrevealscorefunctionalmodulesofstemcellsandpotentialnovelstemnessgenes
AT futschikmatthiase integrationofstemnessgenesignaturesrevealscorefunctionalmodulesofstemcellsandpotentialnovelstemnessgenes