BackgroundFat metabolism in pigs is controlled by tissue-specific molecular mechanisms that ultimately affect growth performance and meat quality. Understanding how epigenetic modifications interact with gene expression across key metabolic and fat-depositing tissues is essential for identifying regulatory processes and potential biomarkers to improve pork quality traits. Therefore, this study aimed to elucidate tissue specific epigenetic regulation of fat metabolism by integrating DNA methylation and gene expression profiles from liver, backfat, and loin (longissimus dorsi) tissues at two physiologically developmental stages (10 and 26 weeks), representing the early post-weaning growth phase and near-market weight, respectively. By explicitly comparing these ages and tissues, the study was designed to capture the transition from muscle-dominated growth to increased lipid deposition and to identify tissue- and stage-specific regulatory signatures that may serve as biomarkers for pork quality.ResultsGenome-wide DNA methylation exhibited weak clustering by tissue, whereas gene expression showed clear tissue separation. The liver harbored fewer genes with differential methylation across stage and tissue but a greater number of genes with differential expression than backfat and loin, suggesting distinct regulatory modes. Integrative analysis of the overlap genes between methylation and expression signals highlighted epigenetically mediated regulation of extracellular matrix organization, lipid metabolism, and muscle development pathways. Furthermore, weighted gene co-expression network analysis revealed distinct tissue-specific correlations between co-methylated and co-expressed modules, with enrichment in cholesterol biosynthesis, muscle contractility, and extracellular matrix remodeling. Together, these findings suggest that methylation changes are more subtle than transcriptional shifts, yet they are aligned with key functional pathways, consistent with a role for methylation as a fine-tuning mechanism that shapes tissue-specific transcriptional networks during growth.ConclusionsAcross liver, backfat, and loin, DNA methylation modulates transcriptional programs in a tissue-dependent manner, prioritizing pathways central to lipid handling, extracellular matrix remodeling, and muscle function. This integrated multi-omics framework highlights candidate epigenetic markers and regulatory modules with potential utility for improving pork quality traits through selection or management strategies.

As pork consumption increases, consumer demand for high-quality meat has also increased. To improve pork quality, minimizing stress throughout the slaughter process is essential. Implementation of animal welfare measures can reduce stress, and the stunning stage, which renders animals unconscious, is crucial for ensuring animal welfare, slaughter efficiency, and final meat quality. Previous studies focused on the changes that occur in physiological and physicochemical characteristics following electrical and gas stunning. Using transcriptome analysis, this study aimed to elucidate the changes in gene expression and molecular-level biological responses to electrical and CO2 gas stunning methods. The two stunning methods (electrical stunning, 10 pigs; CO2-controlled atmosphere stunning, 10 pigs) were compared based on transcriptomic changes determined by whole-blood RNA-Seq. Differentially expressed genes were identified for each group (electrical stunning: 67 upregulated and 37 downregulated genes; CO2-controlled atmosphere stunning: 39 upregulated and 17 downregulated genes). Biological mechanisms associated with pig responses to stunning methods were identified through functional annotation. Under electrical stunning conditions, tissue damage responses such as extracellular matrix stability degradation and potential inflammatory reactions were observed. By contrast, under CO2-gas stunning conditions, defense and physiological regulatory mechanisms to buffer oxidative stress were induced, accompanied by immune balance and tissue protection mechanisms. Our study revealed distinct biological mechanisms underlying pig responses to different stunning methods, suggesting that these mechanisms could serve as a cornerstone for assessing slaughter stress, enhancing meat quality, and improving animal welfare.

Livestock production systems are increasingly constrained by infectious diseases and environmental stress. These factors compromise productivity, animal welfare, and sustainability under heterogeneous field conditions. Immune-related traits governing disease susceptibility, recovery, and performance loss are polygenic and influenced by diverse conditions. They arise from coordinated responses across multiple tissues and molecular layers. As a result, single-omics approaches often fail to generalize across breeds, environments, and management systems, limiting their translational value in improving livestock health. Livestock immunogenomics has emerged as a framework for addressing this complexity by linking genetic variation with regulatory, cellular, and metabolic programs that shape immune competence and resilience across diverse biological and production conditions. In recent years, substantial progress in functional genome annotation, genotype–tissue regulatory atlases, and single-cell reference datasets has strengthened the foundation for systems-level analyses in major livestock species. However, effective translation requires integrative strategies aligned with field-relevant phenotypes and capable of remaining interpretable under varying production and biological conditions. In this review, we synthesized computational and experimental strategies for omics integration in livestock immunogenomics and examined their applications across three major domains: infectious diseases, environmental stress, and xenotransplantation. We highlight design principles that improve interpretability and transportability, including longitudinal sampling, phase-aware designs across stages of the response, compartment-resolved analysis across tissues, integration of regulatory layers, and explicit reduction of complex outputs into deployable signatures. Case studies in cattle, swine, and poultry illustrate how integrative frameworks distinguish protective immune programs from inflammation-associated damage, link molecular modules to resilience-related phenotypes, and support their application in precision health management and breeding strategies. Beyond production systems, we discuss xenotransplantation as an extreme but informative translational setting. In this context, livestock immunogenomics reveals how immune outcomes emerge from coordinated regulatory and metabolic programs rather than from individual antigenic mismatches. Collectively, this review emphasizes that the future impact of livestock immunogenomics lies not in increasing data dimensionality, but treating omics integration as a translational pipeline that connects systems-level immune biology to practical interventions for animal health, welfare, and sustainable production.

Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses in the global swine industry due to its high genetic diversity and different virulence levels, which complicate disease management and vaccine development. This study evaluated longitudinal changes in the immune cell composition of bronchoalveolar lavage fluid and the clinical outcomes across PRRSV strains with varying virulence, using techniques including single-cell transcriptomics. In highly virulent infection, faster viral replication results in an earlier peak lung-damage time point, marked by significant interstitial pneumonia, a significant decrease in macrophages, and an influx of lymphocytes. Viral tracking reveals less than 5% of macrophages are directly infected, and further analysis indicates bystander cell death, likely regulated by exosomal microRNAs as a significant factor. In contrast, the peak intermediate infection shows a delayed lung-damage time point with fewer cell population modifications. Furthermore, anti-inflammatory M2-like macrophages (SPP1-CXCL14high) are identified and their counts increase during the peak lung-damage time point, likely contributing to local defense and lung recovery, which is not observed in high virulent infection. These findings provide a comprehensive description of the immune cellular landscape and differential PRRSV virulence mechanisms, which will help build new hypotheses to understand PRRSV pathogenesis and other respiratory infections.

The first camelized mouse model (Nrap c.255ins78) was developed to explore how camels adapt to extreme environments. Previous studies showed that these mice exhibit a cold‐resistant phenotype, with increased expression of inflammatory cytokine‐related genes in the heart under cold stress. This study aims to build on prior research by analyzing the heart transcriptomes of Nrap c.255ins78 mice under non‐stress conditions to investigate the origins of inflammatory cytokine responses in the heart during cold exposure. For this purpose, RNA sequencing was used to analyze the heart transcriptomes of 12‐week‐old male and female Nrap c.255ins78 mice and control wild‐type mice. As a result, we identified 25 differentially expressed genes between wild‐type and Nrap c.255ins78 mice. Twelve of them were associated with the cell cycle and division, all consistently downregulated in Nrapc.255ins78 mice. The Cib3 (calcium and integrin‐binding protein) gene was significantly upregulated (FDR < 0.05; P < 0.001). These DEGs are linked to altered calcium dynamics in cardiomyocytes, maintaining homeostasis, and suggest that inflammatory cytokines during cold exposure may serve as an adaptive response. Our findings provide insights into the genetic mechanisms underlying temperature adaptation in camels and suggest pathways for enhancing stress resistance in other mammals.

Bisphenol A (BPA) is a widely used xenoestrogen that can disrupt neuroendocrine and immune regulation through multiple hormone receptors. This study investigated BPA-induced long non-coding RNA (lncRNA)-mRNA interactions in the cerebral cortex and hypothalamic-pituitary-thyroid (HPT) axis of adult male mice. Transcriptome sequencing and comprehensive lncRNA annotation identified 14,858 novel lncRNA transcripts. Integrated network analysis using weighted gene co-expression network analysis (WGCNA) revealed four distinct tissue-specific modules: neuronal signaling alterations (Tac1, Htr1b, Npy), RNA splicing modifications (Srsf5), PI3K/Akt-mediated cellular dysfunction (Creb5, Cdkn1a), and immune receptor signaling disruptions (Trbv15, Fcrla). These findings suggest that BPA reprograms transcriptional networks in a tissue-specific manner, potentially disrupting hormone-related neurotransmission, metabolic regulation, and immune signaling via lncRNA-mediated mechanisms. Such systems-level reprogramming of the immune-neuroendocrine network (INEN) provides novel mechanistic insights and biomarker candidates for assessing and mitigating the health impacts of environmental endocrine disruptors.

Porcine reproductive and respiratory syndrome (PRRS) causes significant economic losses in the swine industry. However, the molecular mechanisms behind the common and cell type-specific systemic responses during PRRS virus (PRRSV) infection are not well understood. In this study, we collected viremia data, antibody levels, and whole-blood RNA-seq data obtained from eight PRRSV-infected piglets. We utilised a cell deconvolution approach to calculate cell type enrichment, constructed a time-serial gene co-expression network with differentially expressed genes, and conducted functional annotations. Three significant modules were identified within the network. The changes associated with viremia revealed an upregulated expression of genes related to antiviral activity. In the T-cell- and NK-cell-specific modules, infection led to an increased T-cell population and upregulation of genes related to T-cell defence responses. Conversely, in the monocyte- and neutrophil-specific module, genes involved in inflammatory responses were downregulated due to a decrease in monocyte proportion. This study highlights the time-series antiviral activities associated with viremia and the transcriptomic changes associated with immune responses in specific cell types. The findings provide comprehensive insights into host responses to PRRSV infection, including diagnostic biomarkers.

Background/Objectives: The first camelized mouse model (Nrapc.255ins78) was developed to investigate the mechanisms underlying camels’ adaptation to extreme environments. Previous studies demonstrated that these mice exhibit a cold-resistant phenotype, characterized by increased expression of inflammatory cytokine-related genes in the heart under cold stress. Nebulin-related anchoring protein (NRAP) plays a critical role in organizing myofibrils during cardiomyocyte development. This study builds on prior research by analyzing the heart transcriptomes of Nrapc.255ins78 mice under non-stress conditions to explore the origins of inflammatory cytokine responses during cold exposure. Methods: RNA sequencing was performed on the hearts of 12-week-old male and female Nrapc.255ins78 and wild-type control mice. Results: Differential expression analysis identified 25 genes, including 12 associated with cell cycle and division, all consistently downregulated in Nrapc.255ins78. Notably, the calcium and integrin-binding protein gene (Cib3) was significantly upregulated (FDR < 0.05; p < 0.001). Conclusions: These differentially expressed genes suggest altered calcium dynamics in cardiomyocytes and mechanisms for maintaining homeostasis, supporting the hypothesis that inflammatory cytokines during cold exposure may represent an adaptive response. These findings provide valuable insights into the genetic mechanisms of temperature adaptation in camels and highlight potential pathways for enhancing stress resistance in other mammals.

Understanding molecular characteristics and metabolic processes of the mammalian endometrium is crucial for adva-ncing biological research, particularly in veterinary obstetrics and pathology. This study established and analyzed organoids from endometrial epithelial stem cells of five mammals with different placental types: cows (cotyledonary), dogs and cats (zonary), pigs (diffuse), and rats (discoid). Organoids from these five species were maintained for over 13 passages, frozen, and thawed. Pathological analysis confirmed that they retained chara-cteristics of their original tissues. Furthermore, integrative trans-criptome analysis of organoids and tissues from the five species highlighted key pathways such as PI3K-Akt signaling and extra-cellular matrix-receptor interaction known to be crucial in cancer research. Although genes associated with vascular smooth muscle contraction were downregulated, these organoids exhibited sig-nificant activities of genes involved in hormone metabolism. In conclusion, our study achieved stable establishment of endome-trial organoids from five mammals with different placental types, offering foundational data for organoid research. In the future, these organoids are suitable models for investigating uterine physiology and diseases and for developing potential therapies.

Current therapies for inflammatory bowel disease (IBD) often fail to achieve complete remission and are associated with systemic toxicity owing to their broad immunosuppressive effects. To overcome these limitations, we developed a bioengineered extracellular vesicle (EV) platform that modulates key immune signaling pathways to efficiently restore the T-cell balance in inflamed intestinal tissues. EVs derived from Wharton’s jelly mesenchymal stem cells were engineered to display PD-L1 on their surface and encapsulate miR-27a-3p. Surface PD-L1 engages the PD-1 checkpoint in activated T cells, attenuating T-cell receptor signaling via SHP2-mediated dephosphorylation of ZAP70 and AKT. In parallel, miR-27a-3p suppresses prohibitin 1 (PHB1), a mitochondrial regulator of Th17 cell bioenergetics and inflammatory function, thereby reducing Th17 polarization and increasing the number of FOXP3⁺ regulatory T cells. These dual-targeting EVs preferentially localized to inflamed intestinal tissues via chemokine (CCR2/CXCR4) and PD-1-dependent mechanisms. In humanized mouse models of colitis, these EVs attenuated mucosal inflammation, suppressed effector T-cell responses, and preserved epithelial integrity. In IBD patient-derived colonoid cultures, PD-L1/miR-27a-3p EVs maintained epithelial viability and barrier integrity without inducing cytotoxicity or structural disruption. Transcriptomic and single-cell analyses revealed the downregulation of inflammatory and exhaustion signatures, along with the enrichment of regulatory subsets. Collectively, this study presents a cell-free immunotherapeutic approach that reprograms T cells in inflamed tissues through the PD-1 and mitochondrial signaling pathways while maintaining intestinal epithelial integrity, offering a promising therapeutic strategy for IBD and other T cell-driven inflammatory disorders.

Egg production in laying hens is related to very complex and elaborate processes involving the cooperation of various tissues. Laying hens undergo this complicated production process in different production stages during overall laying periods. However, many previous studies have focused on a single tissue or specific production stage. Thus, we compared multi-tissue transcriptome profiles across different production stages using RNA-seq to understand which overall metabolic changes occur in laying hens as the stage progresses. Laying hens at three distinct production stages of early-phase (EP, 30 wk of age), mid-phase (MP, 46 wk of age), and late-phase (LP, 60 wk of age) were used to analyze transcriptomic changes for the liver, jejunum, and uterus tissues. Weighted gene co-expression network analysis was adopted to detect core modules and central genes, and finally identified 11 co-expression modules. In the liver and jejunum, the expression of genes (e.g., FABP2, FABP7, PPARG) related to fatty acid synthesis was increased with production stages. However, the expression of genes (e.g., GSTA2, BLB1 and BLB2) related to immune responses, including xenobiotic metabolism pathway and the herpes simplex virus 1 infection pathway, was increased in EP compared with other stages. Moreover, the expression of genes related to calcium signaling pathways (e.g., CACNA2D1) and muscle contraction metabolism (e.g., ACTG2 and RYR2) in the uterus was decreased as laying hens were aged. The current findings pave the way for future investigations into the physiological changes in laying hens across different production stages. This research also provides a foundation for elucidating the multi-tissue transcriptome in laying hens and identifying potential genes regulating various biological processes during overall laying periods.

In the poultry industry, the slaughter process poses significant animal welfare concerns due to the substantial stress it induces in broilers. Electrical stunning (ES) and controlled atmosphere stunning (CAS) are commonly used methods to render broilers unconscious before slaughter, but both have welfare implications. This study compares ES and CAS by analyzing stress-related gene expression profiles using RNA sequencing (RNA-seq) and evaluating meat quality parameters. The results reveal distinct molecular responses to each method. Meat quality analysis shows that ES leads to higher redness and fat content, while CAS results in greater moisture content. ES induces physiological stress by causing tissue damage and activating inflammatory pathways, whereas CAS does so through hypercapnia and immune response downregulation, suggesting lower oxidative stress and reduced physiological burden. Future studies should integrate behavioral and neurophysiological assessments, tissue-specific histology, biochemical markers, and comparative evaluations of inert-gas stunning methods (e.g., argon, nitrogen) to better contextualize welfare implications. These findings provide new insights into the molecular and physiological impacts of stunning methods, contributing to the development of more humane poultry production practices.

Camels possess exceptional adaptability, allowing them to withstand extreme temperatures in desert environments. They conserve water by reducing their metabolic rate and regulating body temperature. The heart of the camel plays a crucial role in this adaptation, with specific genes expressed in cardiac tissue that are essential for mammalian adaptation, regulating cardiac function and responding to environmental stressors. One such gene, nebulin-related-anchoring protein (NRAP), is involved in the assembly of myofibrils and the transmission of force within the heart. In our study of the NRAP gene across various livestock species, including three camel species, we identified a camel-specific exon region in the NRAP transcripts. This additional exon (exon 4) contains an open reading frame predicted in camels. To investigate its function, we generated knock-in mice expressing camel NRAP exon 4. These 'camelized mice' exhibited normal phenotypic characteristics compared with wild-type mice but showed elevated body temperatures under cold stress. Transcriptome analyses of the hearts from camelized mice under cold stress revealed differentially expressed inflammatory cytokine genes, known to influence cardiac function by modulating the contractility of cardiac muscle cells. We propose further investigations utilizing these camelized mice to explore these findings in greater depth.

The mechanism of estrous cycles of pigs should be explored because their reproductive traits are useful for manipulating productivity and solving problems such as infertility. These estrous cycles should be elucidated to understand the complex interactions between various reproductive tissues (including the ovary, oviduct, and endometrium) and the complex range of hormone secretions during estrous cycles. Long non-coding RNAs (lncRNAs) regulate target genes at transcriptional, post-transcriptional, and post-translational regulation levels in various species. However, unlike mRNAs, lncRNAs in pigs have not been sufficiently annotated, and understanding the protein level of coding genes has limitations in determining the mechanism of the reproductive traits of porcine. In this study, the lncRNAs of the porcine ovary, oviduct, and endometrium were investigated on days 0, 3, 6, 9, 12, 15, and 18 of the estrous cycle. In addition, the characteristics and functions of the identified lncRNAs were explored. 19,021 novel lncRNA transcripts were selected, and the comparison of the characteristics of the newly identified lncRNA and mRNA showed that similar to those of previous studies. Four lncRNA networks were chosen through network analysis. The cis-acting genes of lncRNAs included in each network were identified, and expression patterns were compared. The main lncRNAs (XLOC_021792, XLOC_017111, ENSSSCG00000050977, XLOC_000342, ENSSSCG00000050380, ENSSSCG00000045111, XLOC_008338, XLOC_004128, and ENSSSCG00000040267) were determined from the network by considering the cis-acting genes. Specific novel lncRNAs were discovered in the reproductive tissues during the swine estrous cycle, and their time-serial expression dynamics were confirmed. As the main lncRNAs are involved in the development of each reproductive tissue and hormone action, they can be utilized as potential biomarkers to help improve and develop the reproductive traits of pigs.

Background: South Korea has recently faced record-high temperatures, which have adversely affected dairy production. Holstein cows, the primary dairy breed globally, are particularly sensitive to heat stress. In contrast, Jersey cows have shown greater heat tolerance, as demonstrated by phenotypic studies. Methods: We investigated physiological and molecular responses to heat stress in Holstein and Jersey cows by measuring rectal temperature, milk yield, and average daily gain, confirming Holstein cows’ greater vulnerability. To explore molecular mechanisms, we analyzed circulating microRNA profiles from whole blood samples collected under heat stress and normal conditions using microRNA-sequencing. Differential expression patterns were compared between the two breeds to identify biological pathways associated with heat stress. Results: Four microRNAs (bta-miR-20b, bta-miR-1246, bta-miR-2284x, and bta-miR- 2284y) were significantly differentially expressed in both breeds under heat stress (|FC| ≥ 2, p < 0.05). Notably, bta-miR-20b and bta-miR-1246 were linked to corpus luteum function and progesterone biosynthesis, while bta-miR-2284x and bta-miR- 2284y were associated with immune responses. A comparison of 11 potential heat stress-related microRNAs identified in previous studies of Holstein cows revealed consistent expression trends in Jersey cows, albeit with lower fold changes, suggesting their superior heat resilience. Conclusions: Our study highlights the physiological and microRNA-based differences in heat stress responses between Holstein and Jersey cows. Jersey cows exhibited greater resilience, supported by more stable microRNA expression profiles and improved heat stress indicators, making them a promising breed for dairy production in increasingly hot climates.