Search Results (13)

Pigs are a major source of animal protein for humans and serve as valuable biomedical models. Compared to Western commercial pig breeds, Jinhua pigs are characterized by superior meat quality due to dynamic muscle development and fat deposition. However, studies investigating dynamic transcriptional regulation of swine meat quality traits across developmental stages remain limited. In this work, we collected longissimus dorsi muscle tissue from three Jinhua and three Landrace × Yorkshire pigs at 1, 90, and 180 days of age, respectively. We have uncovered differentially expressed genes and transcripts, alternative splicing events, and gene fusion events across development stages utilizing RNA sequencing data. CKM exhibited consistent breed-specific alternative splicing and gene fusion events across all three stages, representing a stable regulator of muscle development in Jinhua pigs. On the other hand, our findings highlight day 90 as a critical “window phase” for muscle development and meat quality differences between Jinhua and Landrace × Yorkshire pigs at this stage, exhibiting the greatest number of inter-breed differences in transcriptomic genetic regulation. Additionally, time series analysis revealed that genes with peak expression at day 90 were significantly enriched in pathways associated with muscle development and function. Finally, we identified PFKM, PRKAG3, and CKM as candidate genes with age-specific expression and post-transcriptional regulation that likely influence muscle development. This study advances understanding of transcriptional regulation in pig muscle with implications for meat quality improvement. Full article

The Body Mass Index (BMI), integrating body weight and length, is a widely used metric for obesity assessment in humans. As pigs serve as crucial biomedical models, the application of BMI in swine and its genetic basis remain poorly explored. This study aimed to investigate the genetic architecture of pig BMI and compare two carcass-based BMI metrics (BMI-S and BMI-O) for breeding applicability. A total of 439 Landrace × Yorkshire crossbred pigs were genotyped with a 50 K SNP chip; heritability was estimated via a mixed linear model, and genome-wide association study (GWAS) was performed using the BLINK model. BMI-S and BMI-O exhibited moderate-to-high heritability of 0.55 and 0.47, respectively, with 17 genome-wide significant SNPs detected—including the top associated SNP rs81382440 on chromosome 4 and rs80898583 on chromosome 7. Key candidate genes (GPHN, ADAM33, KCNH8, PDCD4) and 5 SNP-trait associations validated in PigQTLdb were linked to lipid/energy metabolism and muscle development. Carcass-based BMI improved phenotypic accuracy, and our findings provide core genetic markers and a theoretical basis for molecular breeding of pig body conformation and lipid deposition traits. Full article

Porcine peripheral blood mononuclear cells (pPBMCs) are increasingly recognized as a valuable model in biomedical and translational research, particularly in contexts directly related to human health and disease. Their immunological features, such as the presence of CD4⁺CD8⁺ double-positive T cells and cytokine expression patterns, exhibit a notable degree of similarity to human immune cells, making them an attractive tool for studying human-relevant immune responses. This review outlines current methodologies for isolating and cryopreserving pPBMCs, with a focus on maintaining high cell viability and functionality. Key technical considerations, including the optimal use of gradient media, appropriate anticoagulants, and standardized freezing/thawing protocols, are discussed in detail. Furthermore, the article highlights the applications of pPBMCs in various research contexts, including vaccine development, inflammation studies, infection models, and xenotransplantation. A comparative perspective is provided to identify similarities and differences between porcine and human PBMCs, supporting the validity of swine as a translational model. Evidence from pPBMC-based studies has shown predictive value for human outcomes, reinforcing their role as a surrogate system for preclinical investigations. Given their anatomical, physiological, and immunogenetic similarities to humans, porcine PBMCs represent a valuable bridge between basic science and clinical application, playing an increasingly important role in translational medicine. Full article

Traditional pig breeding has improved production traits but faces limitations in genetic diversity, disease resistance, and environmental adaptation. Gene editing technologies, such as CRISPR/Cas9, base editing, and prime editing, enable precise genetic modifications, overcoming these limitations and expanding applications to biomedical research. Here, we reviewed the advancements in gene editing technologies in pigs and explored pathways toward optimized swine genetics for a resilient and adaptive livestock industry. This review synthesizes recent research on gene editing tools applied to pigs, focusing on CRISPR/Cas9 and its derivatives. It examines their impact on critical swine production traits and their role as human disease models. Significant advancements have been made in targeting genes for disease resistance, such as those conferring immunity to porcine reproductive and respiratory syndrome viruses. Additionally, gene-edited pigs are increasingly used as models for human diseases, demonstrating the technology’s broader applications. However, challenges such as off-target effects, ethical concerns, and varying regulatory frameworks remain. Gene editing holds substantial potential for sustainable and productive livestock production by enhancing key traits and supporting biomedical applications. Addressing technical and ethical challenges through integrated approaches will be essential to realize its full potential, ensuring a resilient, ethical, and productive livestock sector for future generations Full article

High consumption of ultra-processed foods, rich in sugar and unhealthy fats, has been linked to the onset of numerous chronic diseases. Consequently, there has been a growing shift towards a fiber-rich diet, abundant in fruits, vegetables, seeds, and nuts, to enhance longevity and quality of life. The primary bioactive components in these plant-based foods are polyphenols, which exert significant effects on modulating the gastrointestinal microbiota through their antioxidant and anti-inflammatory activities. This modulation has preventive effects on neurodegenerative, metabolic, and cardiovascular diseases, and even cancer. The antimicrobial properties of polyphenols against pathogenic bacteria have significantly reduced the need for antibiotics, thereby lowering the risk of antibiotic resistance. This paper advances the field by offering novel insights into the beneficial effects of polyphenols, both directly through the metabolites produced during digestion and indirectly through changes in the host’s gastrointestinal microbiota, uniquely emphasizing swine as a model highly relevant to human health, a topic that, to our knowledge, has not been thoroughly explored in previous reviews. This review also addresses aspects related to both other animal models (mice, rabbits, and rats), and humans, providing guidelines for future research into the benefits of polyphenol consumption. By linking agricultural and biomedical perspectives, it proposes strategies for utilizing these bioactive compounds as therapeutic agents in both veterinary and human health sciences. Full article

Copy number variations (CNVs) critically influence individual genetic diversity and phenotypic traits. In this study, we employed whole-genome resequencing technology to conduct an in-depth analysis of 50 pigs from five local swine populations [Rongchang pig (RC), Wuzhishan pig (WZS), Tibetan pig (T), Yorkshire (YL) and Landrace (LR)], aiming to assess their genetic potential and explore their prospects in the field of animal model applications. We identified a total of 96,466 CNVs, which were subsequently integrated into 7112 non-redundant CNVRs, encompassing 1.3% of the swine genome. Functional enrichment analysis of the genes within these CNVRs revealed significant associations with sensory perception, energy metabolism, and neural-related pathways. Further selective scan analyses of the local pig breeds RC, T, WZS, along with YL and LR, uncovered that for the RC variety, the genes PLA2G10 and ABCA8 were found to be closely related to fat metabolism and cardiovascular health. In the T breed, the genes NCF2 and CSGALNACT1 were associated with immune response and connective tissue characteristics. As for the WZS breed, the genes PLIN4 and CPB2 were primarily linked to fat storage and anti-inflammatory responses. In summary, this research underscores the pivotal role of CNVs in fostering the diversity and adaptive evolution of pig breeds while also offering valuable insights for further exploration of the advantageous genetic traits inherent to China’s local pig breeds. This facilitates the creation of experimental animal models tailored to the specific characteristics of these breeds, contributing to the advancement of livestock and biomedical research. Full article

Besides its importance as a livestock species, pig is increasingly being used as an animal model for biomedical research. Macrophages play critical roles in immunity to pathogens, tissue development, homeostasis and tissue repair. These cells are also primary targets for replication of viruses such as African swine fever virus, classical swine fever virus, and porcine respiratory and reproductive syndrome virus, which can cause huge economic losses to the pig industry. In this article, we review the current status of knowledge on porcine macrophages, starting by reviewing the markers available for their phenotypical characterization and following with the characteristics of the main macrophage populations described in different organs, as well as the effect of polarization conditions on their phenotype and function. We will also review available cell lines suitable for studies on the biology of porcine macrophages and their interaction with pathogens. Full article

Swine is a common model organism for biomedical research. Epigenetic reprogramming in somatic cell nuclear transfer (SCNT) embryos does not fully recapitulate the natural DNA demethylation events at fertilisation. This study aimed to conduct genome-wide methylation profiling to detect differentially methylated regions (DMRs) responsible for epigenetic differences in stem cells that displayed high and low efficiency of SCNT and to elucidate the low efficiency of cloning rate in pigs. Adipose tissue mesenchymal stem cells (AMSC)s lines were isolated from adipose tissue of adult male pigs (n = 20; high-efficiency cells = 10; and low-efficiency cells = 10). Reduced representation bisulfite sequencing (RRBS) was performed on an Illumina HiSeq1500. Paired-end reads were filtered to remove the adapter contamination, and low-quality reads using TrimGalore! Filtered reads were mapped to the reference genome using Bismark. MethylKit was used to identify differentially methylated regions (DMRs) (bases and tiles), showing statistically significant differential methylation between high and low-efficiency AMSCs. Hierarchical cluster analysis according to methylation patterns clearly defined groups with low and high cloning efficiency. We report 3704 bases with statistically significant differences in methylation and 10062 tiles with statistically significant differences in methylation. Most differentially methylated sites are intergenic 62%, 31% are intronic, 4% are in exons, and 4% in promoters. Moreover, 37% of differentially methylated sites are located in known CpG islands (CGIs), and 4% in CpG island shores (CGSs). Full article

Swine are attracting increasing attention as a biomedical model, due to many immunological similarities with humans. However, porcine macrophage polarization has not been extensively analyzed. Therefore, we investigated porcine monocyte-derived macrophages (moMΦ) triggered by either IFN-γ + LPS (classical activation) or by diverse “M2-related” polarizing factors: IL-4, IL-10, TGF-β, and dexamethasone. IFN-γ and LPS polarized moMΦ toward a proinflammatory phenotype, although a significant IL-1Ra response was observed. Exposure to IL-4, IL-10, TGF-β, and dexamethasone gave rise to four distinct phenotypes, all antithetic to IFN-γ and LPS. Some peculiarities were observed: IL-4 and IL-10 both enhanced expression of IL-18, and none of the “M2-related” stimuli induced IL-10 expression. Exposures to TGF-β and dexamethasone were characterized by enhanced levels of TGF-β2, whereas stimulation with dexamethasone, but not TGF-β2, triggered CD163 upregulation and induction of CCL23. Macrophages stimulated with IL-10, TGF-β, or dexamethasone presented decreased abilities to release proinflammatory cytokines in response to TLR2 or TLR3 ligands: IL-10 showed a powerful inhibitory activity for CXCL8 and TNF release, whereas TGF-β provided a strong inhibitory signal for IL-6 production. While our results emphasized porcine macrophage plasticity broadly comparable to human and murine macrophages, they also highlighted some peculiarities in this species. Full article

Swine are regarded as promising biomedical models, but the dynamics of their gastrointestinal microbiome have been much less investigated than that of humans or mice. The aim of this study was to establish an integrated multi-omics protocol to investigate the fecal microbiome of healthy swine. To this end, a preparation and analysis protocol including integrated sample preparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integration linked microbiome composition with function, and metabolic activity with protein inventories, i.e., 16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae and Clostridiaceae. Similar microbiome compositions in feces and colon, but not ileum samples, were observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g., temporal decreased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome constituents. In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomy and functionality of the intestinal microbiome of swine. Full article

In the search of animal stroke models providing translational advantages for biomedical research, pigs are large mammals with interesting brain characteristics and wide social acceptance. Compared to rodents, pigs have human-like highly gyrencephalic brains. In addition, increasingly through phylogeny, animals have more sophisticated white matter connectivity; thus, ratios of white-to-gray matter in humans and pigs are higher than in rodents. Swine models provide the opportunity to study the effect of stroke with emphasis on white matter damage and neuroanatomical changes in connectivity, and their pathophysiological correlate. In addition, the subarachnoid space surrounding the swine brain resembles that of humans. This allows the accumulation of blood and clots in subarachnoid hemorrhage models mimicking the clinical condition. The clot accumulation has been reported to mediate pathological mechanisms known to contribute to infarct progression and final damage in stroke patients. Importantly, swine allows trustworthy tracking of brain damage evolution using the same non-invasive multimodal imaging sequences used in the clinical practice. Moreover, several models of comorbidities and pathologies usually found in stroke patients have recently been established in swine. We review here ischemic and hemorrhagic stroke models reported so far in pigs. The advantages and limitations of each model are also discussed. Full article

Progress in genetic engineering over the past few decades has made it possible to develop methods that have led to the production of transgenic animals. The development of transgenesis has created new directions in research and possibilities for its practical application. Generating transgenic animal species is not only aimed towards accelerating traditional breeding programs and improving animal health and the quality of animal products for consumption but can also be used in biomedicine. Animal studies are conducted to develop models used in gene function and regulation research and the genetic determinants of certain human diseases. Another direction of research, described in this review, focuses on the use of transgenic animals as a source of high-quality biopharmaceuticals, such as recombinant proteins. The further aspect discussed is the use of genetically modified animals as a source of cells, tissues, and organs for transplantation into human recipients, i.e., xenotransplantation. Numerous studies have shown that the pig (Sus scrofa domestica) is the most suitable species both as a research model for human diseases and as an optimal organ donor for xenotransplantation. Short pregnancy, short generation interval, and high litter size make the production of transgenic pigs less time-consuming in comparison with other livestock species This review describes genetically modified pigs used for biomedical research and the future challenges and perspectives for the use of the swine animal models. Full article

The inbred strain of miniature pig is an ideal model for biomedical research due to its high level of homozygosity. In this study, we investigated genetic diversity, relatedness, homozygosity, and heterozygosity using the Porcine SNP60K BeadChip in both inbred and non-inbred Wuzhishan pigs (WZSPs). Our results from multidimensional scaling, admixture, and phylogenetic analyses indicated that the inbred WZSP, with its unique genetic properties, can be utilized as a novel genetic resource for pig genome studies. Inbreeding depression and run of homozygosity (ROH) analyses revealed an average of 61 and 12 ROH regions in the inbred and non-inbred genomes of WZSPs, respectively. By investigating ROH number, length, and distribution across generations, we further briefly studied the impacts of recombination and demography on ROH in these WZSPs. Finally, we explored the SNPs with higher heterozygosity across generations and their potential functional implications in the inbred WZSP. We detected 56 SNPs showing constant heterozygosity with He = 1 across six generations in inbred pigs, while only one was found in the non-inbred population. Among these SNPs, we observed nine SNPs located in swine RefSeq genes, which were found to be involved in signaling and immune processes. Together, our findings indicate that the inbred-specific pattern of homozygosity and heterozygosity in inbred pigs can offer valuable insights for elucidating the mechanisms of inbreeding in farm animals. Full article