Omics & gene networks

Integrated Transcriptomic Analysis of miRNA-Mediated Regulation: Aflatoxin Toxicity and Dietary Herbal Supplementation in the Porcine Liver

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Abstract

Aflatoxin B1 (AFB1), a prevalent mycotoxin, is widely recognized for its potent hepatotoxic and hepatocarcinogenic properties, which lead to significant health detriments in livestock consuming contaminated feed. While the mechanisms of hepatic damage are known, the underlying microRNA (miRNA)-mediated molecular pathways of AFB1 toxicity and the distinct regulatory signatures of dietary herbal supplementation are not fully elucidated. This study aims to investigate the effects of AFB1 and medicinal herb dietary supplements on the porcine liver's miRNA expression profile, characterizing the hepatic regulatory program induced by Andrographis paniculata. To achieve this, we employed a multi-layered miRNA-mRNA interactome analysis to construct a high-confidence map of miRNA-target interactions, deciphering the distinct miRNA-mediated pathways involved in both toxicity and hepatoprotection. Commercial crossbred TN70 pigs (Norsvin Landrace à— Large White; n = 44) underwent 7 days of adaptation before allocation to six treatments: (1) AFB1 + DMSO (120 µg/kg BW; n = 6), (2) Andrographis paniculata (AP) (30 mg/kg BW; n = 10), (3) Silybum marianum (SM) (90 mg/kg BW; n = 10), (4) Curcuma longa (CL) (90 mg/kg BW; n = 10), (5) DMSO (n = 4), and (6) Control (n = 4). Medicinal herbs were administered from day 42, while AFB1 was administered from day 56 until the end of the experiment on day 70. Liver tissues were collected, immediately snap-frozen, and preserved at −80 °C. Total RNA was extracted following a standardized protocol (RIN > 7.0). Matched small RNA and mRNA libraries were prepared from the same liver tissue samples to facilitate intra-individual correlation. A comprehensive bioinformatics pipeline began with differential expression analysis across DESeq2 across several experimental contrasts. To identify functionally active miRNA-target pairs, biophysical predictions were integrated with empirical expression data. Potential binding sites within the 3' UTR, 5' UTR, and CDS of the Sus scrofa genome were predicted using RNAhybrid, filtering for thermodynamic stability (MFE ≤-25 kcal/mol). Simultaneously, a genome-wide Pearson correlation analysis (r ≤ -0.45) identified negatively correlated miRNA-mRNA pairs, capturing canonical post-transcriptional repression. Our results identified 278 high-confidence regulatory interactions in the AP-responsive network involving 20 differentially expressed miRNAs (DEmiRNAs), where ssc-miR-125b and ssc-miR-199a-5p emerged as primary regulatory nodes targeting 56 and 44 mRNAs, respectively. Key targets in the AP network, including MOSPD1, DDX1, and METTL16, were associated with proteasome activity and energy homeostasis. Metabolic pathway analysis using the KEGG database identified a specialized regulatory program primarily modulating GDP binding, glycogen biosynthetic processes, and proteasomal protein catabolism. Furthermore, significant enrichment in RNA catabolic processes and mRNA methyltransferase activity suggests that AP activates a cytoprotective regulatory program involving the stabilization of the epitranscriptome and energy homeostasis, representing a functional contrast to AFB1-induced toxicity.

Keywords: 2026

How to Cite:

Sultana, S., Pareek, C., Kalra, G., Purohit, N., Sharma, P., Asediya, V., Reyer, H., Oster, M., Hadlich, F., Trakooljul, N., Nalpadan, A. A., Ponsusili, S. & Wimmers, K., (2026) “Integrated Transcriptomic Analysis of miRNA-Mediated Regulation: Aflatoxin Toxicity and Dietary Herbal Supplementation in the Porcine Liver”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283497. doi: https://doi.org/10.31274/wcgalp.23504

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