Liu, Tianyuan  ORCID: https://orcid.org/0000-0002-8561-6239, Lei, Rujing, Khan, Ilyas M. and Theobald, Peter ORCID: https://orcid.org/0000-0002-3227-7130
2026.
Tissue identity is the dominant determinant of cross-species transferability of a porcine developmental programme.
BMC Genomics
10.1186/s12864-026-13103-0
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Abstract
Background Reproducibility and cross-species translation using the domestic pig (Sus scrofa) are limited by the lack of a standardised molecular framework for biological maturation: the pig’s developmental tempo differs substantially from the human’s, yet no tissue-resolved transcriptomic staging system exists. Synchronising porcine and human maturation is essential to move preclinical research from descriptive to predictive. Results We built a transcriptomic atlas of porcine development across five tissues (muscle, brain, liver, blood, lung) from 1,924 PigGTEx RNA-seq profiles. A single partial-least-squares (PLS) regressor staged each tissue at its native ordinal resolution and also drove cross-species transfer and biomarker extraction. Our central result: transfer of a pig-trained developmental score to other species is dominated by tissue identity, with phylogenetic distance a weaker secondary effect. Projected onto the seven-species Cardoso-Moreira atlas, transfer was strongest for brain and heart (–0.92) and weakest for the labile liver and ovary ( and 0.42). Brain and heart stayed high even from pig to chicken ( across 320 Myr), whereas liver and ovary collapsed. A variance partition confirmed the ranking (organ Type-II , ; phylogeny significant only at the species level, Spearman , , ). The score independently confirmed lung, muscle, and adipose on the human dGTEx resource (–0.67) against an ortholog-scramble null and three controls. Because it is fit on pig and projected onto foreign-batch atlases, the transfer cannot arise from a pig-side artefact. A web application is available at https://pigdevstage.streamlit.app. Conclusions The porcine developmental programme transfers to humans and more distant amniotes in a tissue-dependent manner, so the pig’s value as a developmental model is set by how conserved each organ’s developmental logic is, not by phylogenetic proximity. Validated on foreign-species atlases, the transfer sidesteps the stage–study confound that bounds within-pig staging to muscle and liver. The atlas is therefore best used organ by organ: strong for conserved organs (brain, heart) and weak for labile ones (liver).
| Item Type: | Article |
|---|---|
| Date Type: | Published Online |
| Status: | In Press |
| Schools: | Schools > Engineering |
| Publisher: | BioMed Central |
| Date of First Compliant Deposit: | 10 July 2026 |
| Date of Acceptance: | 17 June 2026 |
| Last Modified: | 02 Sep 2026 14:07 |
| URI: | https://orca.cardiff.ac.uk/id/eprint/188136 |
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