In vitro versus in vivo models of kidney fibrosis: Time-course experimental design is crucial to avoid misinterpretations of gene expression data

Shiva Moein; Kobra Moradzadeh; Shaghayegh Haghjooy Javanmard; Seyed Mahdi Nasiri; Yousof Gheisari

doi:10.4103/jrms.JRMS_906_19

In vitro versus in vivo models of kidney fibrosis: Time-course experimental design is crucial to avoid misinterpretations of gene expression data

J Res Med Sci. 2020 Sep 30:25:84. doi: 10.4103/jrms.JRMS_906_19. eCollection 2020.

Authors

Shiva Moein¹, Kobra Moradzadeh¹, Shaghayegh Haghjooy Javanmard², Seyed Mahdi Nasiri³, Yousof Gheisari^{1

4}

Affiliations

¹ Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran.
² Applied Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
³ Department of Clinical Pathology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
⁴ Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.

Abstract

Background: In vitro models are common tools in nephrology research. However, their validity has rarely been scrutinized.

Materials and methods: Considering the critical role of transforming growth factor (TGF)-β and hypoxia pathways in kidney fibrosis, kidney-derived cells were exposed to TGF-β and/or hypoxic conditions and the expression levels of some genes related to these two signaling pathways were quantified in a time-course manner. Furthermore, a unilateral ureteral obstruction mouse model was generated, and the expressions of the same genes were assessed.

Results: In all in vitro experimental groups, the expression of the genes was noisy with no consistent pattern. However, in the animal model, TGF-β pathway-related genes demonstrated considerable overexpression in the ureteral obstruction group compared with the sham controls. Interestingly, hypoxia pathway genes had prominent fluctuations with very similar patterns in both animal groups, suggesting a periodical pattern not affected by the intervention.

Conclusion: The findings of this study suggest that in vitro findings should be interpreted cautiously and if possible are substituted or supported by animal models that are more consistent and reliable. Furthermore, we underscore the importance of time-course evaluation of both case and control groups in gene expression studies to avoid misconceptions caused by gene expression noise or intrinsic rhythms.

Keywords: Chronic kidney failure; hypoxia pathway; rhythmic behavior; time-course analysis; transforming growth factor-β pathway.