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Sex bias evaluation of classic and novel Housekeeping Genes in adipose tissue through the massive analysis of transcriptomics data

Maria Guaita-Cespedes, View ORCID ProfileRubén Grillo-Risco, View ORCID ProfileMarta R. Hidalgo, Sonia Fernández-Veledo, Deborah Burks, View ORCID ProfileMaría de la Iglesia-Vayá, View ORCID ProfileAmparo Galán, View ORCID ProfileFrancisco Garcia-Garcia
doi: https://doi.org/10.1101/2021.12.04.471124
Maria Guaita-Cespedes
1Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), Valencia, 46012, Spain
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Rubén Grillo-Risco
1Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), Valencia, 46012, Spain
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  • ORCID record for Rubén Grillo-Risco
Marta R. Hidalgo
1Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), Valencia, 46012, Spain
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Sonia Fernández-Veledo
2Department of Endocrinology and Nutrition and Research Unit, University Hospital of Tarragona Joan XXIII, Institut d’Investigaciò Sanitària Pere Virgili (IISPV), Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
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Deborah Burks
3Molecular Neuroendocrinology Unit, Principe Felipe Research Center (CIPF), Valencia, 46012, Spain
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María de la Iglesia-Vayá
4Biomedical Imaging Unit FISABIO-CIPF, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, 46012, Valencia, Spain
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Amparo Galán
3Molecular Neuroendocrinology Unit, Principe Felipe Research Center (CIPF), Valencia, 46012, Spain
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  • For correspondence: agalan@cipf.es fgarcia@cipf.es
Francisco Garcia-Garcia
1Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), Valencia, 46012, Spain
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  • ORCID record for Francisco Garcia-Garcia
  • For correspondence: agalan@cipf.es fgarcia@cipf.es
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ABSTRACT

Housekeeping genes (HKG), those involved in the maintenance of basic cell functions, are considered to have constant expression levels in all cell types, and are therefore commonly used as internal controls in gene expression studies. Nevertheless, multiple studies have shown that not all of them have stable expression levels across different cells, tissues, and conditions, introducing a systematic error in the experimental results. The proper selection and validation of control housekeeping genes in the specific studied conditions is crucial for the validity of the obtained results, although, up to date, sex has never been taken into account as a biological variable.

In this work, we evaluate the expression profiles of six classical housekeeping genes, (four metabolic: HPRT, GAPDH, PPIA and UBC, and two ribosomal: 18S and RPL19) used as controls in several tissues, to determine the stability of their expression in adipose tissue of Homo sapiens and Mus musculus and asses sex bias and control suitability. We also evaluated gene expression stability of the genes included in different whole transcriptome microarrays available at the Gene Expression Omnibus database (GEO), to identify new genes suitable to be used as sex-unbiased controls. We perform a sex-based analysis to test for/reveal sexual dimorphism of mRNA expression stability.

We use a novel computational strategy based on meta-analysis techniques which evidence that some classical housekeeping genes do not fit to analyze human adipose tissue when sex variable is included. For instance, the extensively used 18S has shown to be variable in this tissue, while PPIA and RPL19 have shown to be good HKG targets. Further, we propose new sex-unbiased human and mouse housekeeping genes, derived from sex-specific expression profiles, including, RPS8 or UBB. All the results generated in this work are available in an open web resource (https://bioinfo.cipf.es/metafun-HKG), so that they can be consulted and used in further studies.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted December 04, 2021.
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Sex bias evaluation of classic and novel Housekeeping Genes in adipose tissue through the massive analysis of transcriptomics data
Maria Guaita-Cespedes, Rubén Grillo-Risco, Marta R. Hidalgo, Sonia Fernández-Veledo, Deborah Burks, María de la Iglesia-Vayá, Amparo Galán, Francisco Garcia-Garcia
bioRxiv 2021.12.04.471124; doi: https://doi.org/10.1101/2021.12.04.471124
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Sex bias evaluation of classic and novel Housekeeping Genes in adipose tissue through the massive analysis of transcriptomics data
Maria Guaita-Cespedes, Rubén Grillo-Risco, Marta R. Hidalgo, Sonia Fernández-Veledo, Deborah Burks, María de la Iglesia-Vayá, Amparo Galán, Francisco Garcia-Garcia
bioRxiv 2021.12.04.471124; doi: https://doi.org/10.1101/2021.12.04.471124

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