Location: Animal Parasitic Diseases Laboratory
2025 Annual Report
Objectives
Objective 1: Develop immunologic tools to evaluate swine immunity.
Sub-objective 1.A: Develop immunological assays and validate their use for assessing host immune responses to infectious diseases and vaccination.
Sub-objective 1.B: Use immunological tools to inform the design of novel innate immune intervention strategies to treat respiratory diseases of swine.
Objective 2: Elucidate immune and genomic determinants of host responses associated with porcine reproductive and respiratory syndrome virus infection.
Sub-objective 2.A: Discover genetic and biological determinants associated with fetal susceptibility, resilience, or resistance to porcine reproductive and respiratory syndrome.
Sub-objective 2.B: Discover genetic and biological determinants associated with good responders to porcine reproductive and respiratory syndrome vaccines.
Approach
This project will produce new reagents for analyses of swine immunity. This will include characterization of monoclonal antibodies (mAbs) reactive with swine cytokines and chemokines and development of assays that quantify their reactivity. These efforts will be coupled with NIFA grant supported Swine Toolkit efforts. Once characterized commercial access to these mAbs will be coordinated through ARS Technology Transfer Office. Basic studies will be expanded by establishing molecular tools to evaluate gene expression using NanoString Technologies, with codesets developed to explore relative importance of specific tissues and unique cell subsets in disease responses and pathogen resistance. These tools will help to identify alternate biomarkers for risk analyses to assess the impact of respiratory diseases and vaccine efficacy.
This project will apply the use of these innovative, next-generation, genomic, transcriptomic, and immunologic techniques to address Porcine Reproductive and Respiratory Syndrome (PRRS), focusing on our unique sample resources collected via the PRRS Host Genetics Consortium and the Canadian Pregnant Gilt Model projects. We will evaluate the influence of host genetics on antiviral response pathways and will aim to identify critical biomarkers of protective vaccine and infection responses. We will use RNAseq data analyses to provide a more complete picture and reveal details of regulatory mechanisms impacting pig responses to vaccination, viral infection, and differential growth effects. Advanced bioinformatics will be combined with new molecular studies, as well as previously collected genotypic and phenotypic data, to identify pathways and biomarkers associated with protective immune responses to respiratory and reproductive diseases that cause significant losses to the pork industry.
This project will provide alternate resources for improved respiratory disease control and elimination strategies. Overall, our project will inform vaccine evaluation and virus control strategies, identify disease-resistant pigs, and stimulate advances that may be of broad economic importance to pig breeders and the animal health industry.
Progress Report
Supporting Objective 1, we characterized reagents useful for monitoring swine immunity; these enable veterinarians and scientists to document pig health and the effects of vaccine and disease treatments. They also support biomedical research using the pig model. Researchers at Beltsville, Maryland, characterized panels of monoclonal antibodies (mAbs) reactive with swine immune proteins (cytokines, chemokines). They shared mAb proteins with colleagues internationally and worked on long-term repository. They prepared nucleic acids from stored hybridomas (cells that express the mAbs) and provided them for sequencing by international partners in the United Kingdom. These data will then serve as a long-term resource for using advanced technologies to express each mAb for decades to come.
Supporting Objective 2, we forged progress in understanding the effects of porcine reproductive and respiratory syndrome virus (PRRSV) infections, the most economically important pathogen of pigs worldwide. PRRS causes over $600 million in annual losses to the U.S. pig industry. Scientists in Beltsville, Maryland, worked with university researchers to probe fetal responses to PRRSV infection of the sow late in gestation when the virus can be transmitted from the sow to her fetuses. Fetal anti-viral responses vary greatly within the litter; litters can include uninfected fetuses, those harboring high viral levels, and neighboring dead fetuses. We concentrated on placental factors that predict disease severity and death or, instead, fetal resistance to infection. We used focused molecular tests (NanoString codesets) to verify estimates of RNA gene expression. We identified specific genes expressed by susceptible versus resilient fetuses, probing for biomarkers that may help select for PRRS-resistant breeding stock.
Accomplishments
1. Discovered genes that lead to fetal death from congenital viral infections. Porcine reproductive and respiratory syndrome virus (PRRSV) infection during late gestation results in fetal weakness and death for some fetuses while others in the same litter are resilient and show limited effects. The mechanisms leading to fetal compromise are not completely understood. Therefore, ARS researchers in Beltsville, Maryland, worked with university partners to assess expression patterns of targeted placental structural genes and metal (potassium, sodium) transporter-related genes. The level of genes involved in the transport of glucose, amino acids and fatty acid decreased as viral levels increased in the susceptible pig fetus. Data indicated that fetal viral levels drive transcriptional dysregulation of the fetal placenta. These results generally imply that susceptible fetuses experience altered metal ion transport, placental structural integrity, and reduced blood vessel formation, contributing to fetal demise. Based on this data, pig breeders could select sows with improved transporter gene variants, this would increase the likelihood of their fetuses surviving congenital PRRSV infections.
2. Improved swine genome annotation. More than 31 sequenced pig genomes are publicly available. To properly Interpret genomic data, scientists need detailed and accurate annotations of every individual gene. Analysis of incomplete genome versions can lead to incorrect biological interpretations. This information is available for human and mouse genomes. ARS researchers in Beltsville, Maryland, therefore, manually assembled and annotated a non-redundant 16,146 RNA and 15,613 pig protein sequence library, based on the three most complete published swine genomes. They used these data to identify swine genes that are the equivalent, termed orthologous, sequences in mouse and humans to improve the annotation of the swine functional genome. The swine protein library identified 1:1 orthology to 16,496 mouse and 15,770 human proteins and noted that 73.8% of these proteins were conserved among all three species. In fact, when a gene was missing from one of the three genomes, pigs were five times more likely to exclusively share a gene with humans than with mice, indicating the swine as a closer relative to humans. These data strongly validate swine as a scientifically important intermediate species (as good or better than mice) for human biomedical studies. This increased knowledge of the similarity of the swine to the human genome provides support for clinicians and researchers to perform preliminary biomedical studies in swine, rather than mice. This should result in validation of alternative therapies for testing by clinicians for human disease resistance and improved human health.
3. Proposed the Farm Animal Genotype–Tissue Expression (FarmGTEx) Project. The international FarmGTEx Project aims to elucidate the actual details, or genetic determinants, that control gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes (genetic based differences) and phenotypes (actual characteristics) in farmed animals. For each species, the aim of the FarmGTEx Project is to collect multiple types of genetic data, particularly genomics and transcriptomics, specifically from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. ARS researchers in Beltsville, Maryland provided important pig viral disease response transcriptomic datasets for this Project. The Project advocates for coordinated strategies of data analysis and resource-sharing initiatives. These data will serve as a platform for investigating context-specific regulatory effects, which deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by the FarmGTEx Project contribute to improving sustainable agriculture-based food systems, including precision animal breeding, food security, and human biomedicine, ultimately helping farmers and breeders to raise healthier, more productive animals, which in turn helps provide safe and affordable food for all Americans.
4. Organized a repository for livestock immunology reagents. Decades of effort by veterinary researchers generated monoclonal antibodies (mAbs) reactive against many immune proteins (cell markers, cytokines and chemokines) from livestock. Unfortunately, their limited commercial market threatens their long-term availability to clinicians, researchers, and pharmaceutical companies who might benefit from them. Therefore, ARS scientists in Beltsville, Maryland, and Manhattan, Kansas, surveyed their availability and devised a plan for long-term maintenance and storage of hybridomas (cells that express mAbs) and mAbs for veterinary species. Reagents reactive with cattle, sheep, swine, and chicken immune cells and proteins require such a repository. As a result, valuable immune reagents will be securely stored and available for future researchers who will access them for their veterinary disease and vaccine studies. As it is implemented, this plan will ensure lasting benefits to animal health, welfare, and public health by developing tools to track advanced targeted biologic therapies for animal diseases, offering more precise, effective and convenient treatment options.
5. Proposed transdisciplinary initiatives help to advance controlled environment agriculture (CEA). Threats such as seasonal weather changes, limited arable land, economic volatility, and shrinking water resources influence farmers’ ability to maintain a safe and resilient food supply. One promising solution to address these threats is CEA. ARS scientists at Beltsville, Maryland, coordinated an effort for federal agencies to identify and lead multi-agency, transdisciplinary initiatives to advance CEA. As agricultural challenges increase in complexity, proposed solutions are increasingly comprehensive and cross-cutting. The CEA industry contains elements of technology, energy, crop yields, and more; as such, research in this space requires expertise spanning federal agencies and their respective stakeholders. Multi-agency collaboration will provide opportunities to create pathways for robust research coordination for CEA research, programming, and funding. Inter-agency collaboration could extend an individual agency’s reach to different types of stakeholders and may facilitate more interactions with foundations, industry, and the research community as a whole. Such robust, federal cross-cutting scientific collaborations are essential to solving existing and future agricultural challenges.
Review Publications
Fang, L., Teng, J., Lin, Q., Bai, Z., Liu, S., Guan, D., Li, B., Gao, Y., Hou, Y., Gong, M., Pan, Z., Yu, Y., Clark, E., Smith, J., Rawlik, K., Xiang, R., Chamberlain, A.J., Goddard, M.E., Littlejohn, M., Larson, G., Machugh, D.E., O’Grady, J.F., Sorensen, P., Sahana, G., Lund, M., Jiang, Z., Pan, X., Gong, W., Zhang, H., He, X., Zhang, Y., Gao, N., He, J., Yi, G., Liu, Y., Zhao, P., Zhou, Y., Wang, X., Young, R.S., Xia, C., Cheng, H., Ma, L., Cole, J.B., Baldwin, R.L., Li, C., Van Tassell, C.P., Lunney, J.K., Liu, W., Guan, L., Zhao, X., Ibeagha-Awemu, E., Luo, O., Lin, L., Canela-Xandri, O., Derks, M., Crooijmans, R., Godia, M., Madsen, O., Groenen, M., Koltes, J.E., Tuggle, C.K., Mccarthy, F.M., Rocha, D., Amills, M., Clop, A., Ballester, M., Tosser-Klopp, G., Li, J., Fang, C., Fang, M., Wang, Q., Hou, Z., Wang, Q., Zhao, F., Jiang, L., Zhao, G., Zhou, Z., Zhou, R., Liu, H., Li, M., Mo, D., Liu, X., Chen, Y., Yuan, X., Li, J., Zhao, S., Ding, X., Sun, D., Sun, H., Li, C., Jiang, Y., Wu, D., Wang, W., Fan, X., Zhang, Q., Li, K., Yang, N., Hu, X., Liu, G. 2025. The farm animal genotype-tissue expression (FarmGTEx) project. Nature Genetics. https://doi.org/10.1038/s41588-025-02121-5.
Van Goor, A.G., Pasternak, J.A., Walker, K.E., Chick, S.T., Harding, J.C., Lunney, J.K. 2025. Altered structural and transporter-related gene expression patterns in the placenta play a role in fetal demise during Porcine reproductive and respiratory syndrome virus infection. BMC Genomics. 26. Article e279. https://doi.org/10.1186/s12864-025-11397-0.
Boyd, A., Zankowski, P., Wheeler, R., Stokes-Draut, J., Chudnovsky, Y., Ingram, D., Tijerina, M., Mickens, M., Steward, D., Armstrong, K., Boggs, A., Neely, B., Lunney, J.K., Luo, Y. 2025. Controlled environment agriculture: An opportunity to strengthen interagency research collaboration in the US government. Proceedings of the National Academy of Sciences-Nexus. 4(6). Article epgaf155. https://doi.org/10.1093/pnasnexus/pgaf155.