Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans

Biomolecules. 2022 Jun 20;12(6):859. doi: 10.3390/biom12060859.

Abstract

The heart is a significant organ in mammalian life, and the heartbeat mechanism has been an essential focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that determine species differences. Here, we analyzed transcriptome data in mouse, rat, and human atria, ventricles, and sinoatrial nodes (SA) obtained from different platforms and compared them by calculating specificity measure (SPM) values in consideration of species differences. Among the three heart regions, the species differences in SA were the greatest, and we searched for genes that determined the essential characteristics of SA, which was SHOX2 in our criteria. The SPM value of SHOX2 was prominently high across species. Similarly, by calculating SPM values, we identified 3 atrial-specific, 11 ventricular-specific, and 17 SA-specific markers. Ontology analysis identified 70 cardiac region- and species-specific ontologies. These results suggest that reanalyzing existing data by calculating SPM values may identify novel tissue-specific genes and species-dependent gene expression. This study identified the importance of SHOX2 as an SA-specific transcription factor, a novel cardiac regional marker, and species-dependent ontologies.

Keywords: SHOX2; heart; transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Gene Expression Regulation, Developmental
  • Homeodomain Proteins* / genetics
  • Homeodomain Proteins* / metabolism
  • Humans
  • Mice
  • Rats
  • Sinoatrial Node / metabolism
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcriptome*

Substances

  • Homeodomain Proteins
  • Transcription Factors

Grants and funding

This research was funded by JSPS KAKENHI (Grant-in-Aid for Young Scientists (B)), grant numbers 17H15554 and 20K16116 to Y.O., JSPS KAKENHI Grant-in-Aid for Research Activity Start-up (Grant number 21K21316) to D.O., and by collaboration with Ono Pharmaceutical Cooperation, Ltd. (Japan).