Multi-omics insights into functional alterations of the liver in growth-retarded offspring: transcriptomic, epigenetic and metabolomic profiles
Abstract Background Growth retardation is a globally prevalent clinical issue, particularly in preterm offspring. It frequently occurs during the early postnatal development of piglets and results in high mortality. In addition to slow postnatal growth caused by complications from immature organs, t...
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| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-08-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-025-11896-0 |
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| Summary: | Abstract Background Growth retardation is a globally prevalent clinical issue, particularly in preterm offspring. It frequently occurs during the early postnatal development of piglets and results in high mortality. In addition to slow postnatal growth caused by complications from immature organs, these offspring are also at risk of facing significant long-term health challenges in adulthood. The liver plays a crucial role in regulating nutrient metabolism and immune function and frequently communicates with other organs to maintain overall health. However, the multifaceted mechanisms by which the liver regulates growth retardation in offspring remain largely unexplored. Results Here, we selected piglets exhibiting extreme weight variations at both birth and weaning stages for comprehensive histomorphological and multi-omics analysis in the liver. Compared to high weaning weight (HWW) piglets, the liver of low weaning weight (LWW) piglets was predominantly characterized by hepatic vacuolation and structural lesions. Transcriptomic analysis of the liver indicated that differentially expressed genes (DEGs) linked to amino acid metabolism (IDO1, DAO, and UROC1) and innate immune (ISG15, RSAD2, and IFIT1) showed significant upregulation in the high birth weight (HBW) piglets when compared to the low birth weight (LBW) piglets. Furthermore, DEGs identified at the weaning stage are primarily enriched in PPAR signaling pathway, protein digestion and absorption, glutathione metabolism, tryptophan metabolism, and ferroptosis. Notably, ferroptosis was the only pathway that showed overlapping enrichment in the KEGG enrichment analysis across all three omics datasets. Gene GCLM and significantly differential metabolites (SDMs) (L-glutathione, L-cysteine, and Gamma-glutamylcysteine) were co-enriched in ferroptosis and showed higher levels in HWW piglets. The elevation of these genes and metabolites plays a key role in scavenging reactive oxygen species (ROS) accumulation and suppressing hepatic ferroptosis. Notably, GCLM was positively associated with L-glutathione and Gamma-glutamylcysteine, and these two metabolites were positively correlated with weaning weight, implying a potential role of these metabolites in improving growth performance. Finally, integrative analysis of RNA-seq and ATAC-seq data revealed several differentially accessible regions (DARs), which were annotated to the genes ACSL3, ITGA11, COL6A3, CYP2C49, and STXBP3. The transcription factor (TF)-gene regulatory network revealed that five DEGs (PML, STAT1, RCOR2, ELF3, and IRF1) are the downstream target genes of TFs, including MAZ and KIF1. These target DEGs are involved in liver development and the pathogenesis of hepatic disease. Conclusions Taken together, the genes and metabolites identified in this study provide gene-targeted and nutrition-based therapeutic strategies for piglets with growth limitations during the lactation and even post-weaning stages. Our findings also provide epigenetic insights into the molecular mechanisms underlying liver-mediated modulation of growth and development in offspring. |
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| ISSN: | 1471-2164 |