Proteomics Applied to Avian Herpesviruses

V. S, Sekhar Mukhopadhyay C, Kashyap N, Sharma V, Singh N, Salajegheh Tazerji S, Kalantari R, Hajipour P, Singh Malik Y. Animal Wellness: The Power of Multiomics and Integrative Strategies: Multiomics in Improving Animal Health

The livestock industry faces significant challenges, with disease outbreaks being a particularly devastating issue. These diseases can disrupt the food supply chain and the livelihoods of those involved in the sector. To address this, there is a growing need to enhance the health and well-being of livestock animals, ultimately improving their performance while minimizing their environmental impact. To tackle the considerable challenge posed by disease epidemics, multiomics approaches offer an excellent opportunity for scientists, breeders, and policymakers to gain a comprehensive understanding of animal biology, pathogens, and their genetic makeup. This understanding is crucial for enhancing the health of livestock animals. Multiomic approaches, including phenomics, genomics, epigenomics, metabolomics, proteomics, transcriptomics, microbiomics, and metaproteomics, are widely employed to assess and enhance animal health. High-throughput phenotypic data collection allows for the measurement of various fitness traits, both discrete and continuous, which, when mathematically combined, define the overall health and resilience of animals, including their ability to withstand diseases. Omics methods are routinely used to identify genes involved in host-pathogen interactions, assess fitness traits, and pinpoint animals with disease resistance. Genome-wide association studies (GWAS) help identify the genetic factors associated with health status, heat stress tolerance, disease resistance, and other health-related characteristics, including the estimation of breeding value. Furthermore, the interaction between hosts and pathogens, as observed through the assessment of host gut microbiota, plays a crucial role in shaping animal health and, consequently, their performance. Integrating and analyzing various heterogeneous datasets to gain deeper insights into biological systems is a challenging task that necessitates the use of innovative tools. Initiatives like MiBiOmics, which facilitate the visualization, analysis, integration, and exploration of multiomics data, are expected to improve prediction accuracy and identify robust biomarkers linked to animal health. In this review, we discuss the details of multiomics concerning the health and well-being of livestock animals.

Marek's Disease Virus and Reticuloendotheliosis Virus Coinfection Enhances Viral Replication and Alters Cellular Protein Profiles

Coinfection with Marek's disease virus (MDV) and reticuloendotheliosis virus (REV) causes synergistic pathogenic effects and serious losses to the poultry industry. However, whether there is a synergism between the two viruses in viral replication and the roles of host factors in regulating MDV and REV coinfection remains elusive. In this study, we found that MDV and REV coinfection increased viral replication in coinfected cells as compared to a single infection in a limited period. Further, we explore the host cell responses to MDV and REV coinfection using tandem mass tag (TMT) peptide labeling coupled with liquid chromatography–tandem mass spectrometry (LC-MS/MS). Compared with MDV/REV-infected cells, 38 proteins increased (fold change > 1.2) and 60 decreased (fold change < 0.83) their abundance in MDV and REV coinfected cells. Differentially accumulated proteins (DAPs) were involved in important biological processes involved in the immune system process, cell adhesion and migration, cellular processes, and multicellular organismal systems. STRING analysis found that IRF7, MX1, TIMP3, and AKT1 may be associated with MDV and REV synergistic replication in chicken embryo fibroblasts (CEFs). Western blotting analysis showed that the selected DAPs were identical to the quantitative proteomics data. Taken together, we verified that MDV and REV can synergistically replicate in coinfected cells and revealed the host molecules involved in it. However, the synergistic pathogenesis of MDV and REV needs to be further studied.

Applications of mass spectrometry imaging in virus research

Mass spectrometry imaging (MSI) is a label-free molecular imaging technique allowing an untargeted detection of a broad range of biomolecules and xenobiotics. MSI enables imaging of the spatial distribution of proteins, peptides, lipids and metabolites from a wide range of samples. To date, this technique is commonly applied to tissue sections in cancer diagnostics and biomarker development, but also molecular histology in general. Advances in the methodology and bioinformatics improved the resolution of MS images below the single cell level and increased the flexibility of the workflow. However, MSI-based research in virology is just starting to gain momentum and its full potential has not been exploited yet. In this review, we discuss the main applications of MSI in virology. We review important aspects of matrix-assisted laser desorption/ionization (MALDI) MSI, the most widely used MSI technique in virology. In addition, we summarize relevant literature on MSI studies that aim to unravel virus-host interactions and virus pathogenesis, to elucidate antiviral drug kinetics and to improve current viral disease diagnostics. Collectively, these studies strongly improve our general understanding of virus-induced changes in the proteome, metabolome and metabolite distribution in host tissues of humans, animals and plants upon infection. Furthermore, latest MSI research provided important insights into the drug distribution and distribution kinetics, especially in antiretroviral research. Finally, MSI-based investigations of oncogenic viruses greatly increased our knowledge on tumor mass signatures and facilitated the identification of cancer biomarkers.

Proteogenomic Identification of a Novel Protein-Encoding Gene in Bovine Herpesvirus 1 That Is Expressed during Productive Infection

Bovine herpesvirus 1 (BoHV-1) is one of several microbes that contributes to the development of the bovine respiratory disease (BRD) and can also induce abortions in cattle. As other alpha-herpesvirinae subfamily members, BoHV-1 efficiently replicates in many cell types and subsequently establishes a life-long latent infection in sensory neurons. BoHV-1 encodes more than 70 proteins that are expressed in a well-defined manner during productive infection. However, in silico open reading frame (ORF) prediction of the BoHV-1 genome suggests that the virus may encode more than one hundred proteins. In this study we used mass spectrometry followed by proteogenomic mapping to reveal the existence of 92 peptides that map to previously un-annotated regions of the viral genome. Twenty-one of the newly termed “intergenic peptides” were predicted to have a viable ORF around them. Twelve of these produced an mRNA transcript as demonstrated by strand-specific RT-PCR. We further characterized the 5′ and 3′ termini of one mRNA transcript, ORF-A, and detected a 55 kDa protein produced during active infection using a custom-synthesized antibody. We conclude that the coding potential of BoHV-1 is underestimated.

Animal board invited review: advances in proteomics for animal and food sciences

Animal production and health (APH) is an important sector in the world economy, representing a large proportion of the budget of all member states in the European Union and in other continents. APH is a highly competitive sector with a strong emphasis on innovation and, albeit with country to country variations, on scientific research. Proteomics (the study of all proteins present in a given tissue or fluid - i.e. the proteome) has an enormous potential when applied to APH. Nevertheless, for a variety of reasons and in contrast to disciplines such as plant sciences or human biomedicine, such potential is only now being tapped. To counter such limited usage, 6 years ago we created a consortium dedicated to the applications of Proteomics to APH, specifically in the form of a Cooperation in Science and Technology (COST) Action, termed FA1002--Proteomics in Farm Animals: www.cost-faproteomics.org. In 4 years, the consortium quickly enlarged to a total of 31 countries in Europe, as well as Israel, Argentina, Australia and New Zealand. This article has a triple purpose. First, we aim to provide clear examples on the applications and benefits of the use of proteomics in all aspects related to APH. Second, we provide insights and possibilities on the new trends and objectives for APH proteomics applications and technologies for the years to come. Finally, we provide an overview and balance of the major activities and accomplishments of the COST Action on Farm Animal Proteomics. These include activities such as the organization of seminars, workshops and major scientific conferences, organization of summer schools, financing Short-Term Scientific Missions (STSMs) and the generation of scientific literature. Overall, the Action has attained all of the proposed objectives and has made considerable difference by putting proteomics on the global map for animal and veterinary researchers in general and by contributing significantly to reduce the East-West and North-South gaps existing in the European farm animal research. Future activities of significance in the field of scientific research, involving members of the action, as well as others, will likely be established in the future.

Marek's disease virus-encoded analog of microRNA-155 activates the oncogene c-Myc by targeting LTBP1 and suppressing the TGF-β signaling pathway

Marek's disease virus (MDV) is a representative alpha herpes virus able to induce rapid-onset T-cell lymphoma in its natural host and regarded as an ideal model for the study of virus-induced tumorigenesis. Recent studies have shown that the mdv1-miR-M4-5p, a viral analog of cellular miR-155, is critical for MDV׳s oncogenicity. However, the precise mechanism whereby it was involved in MD lymphomagenesis remained unknown. We have presently identified the host mRNA targets of mdv1-miR-M4-5 and identified the latent TGF-β binding protein 1 (LTBP1) as a critical target for it. We found that during MDV infection, down-regulation of LTBP1 expression by mdv1-miR-M4-5p led to a significant decrease of the secretion and activation of TGF-β1, with suppression of TGF-β signaling and a significant activation of expression of c-Myc, a well-known oncogene which is critical for virus-induced tumorigenesis. Our findings reveal a novel and important mechanism of how mdv1-miR-M4-5p potentially contributes to MDV-induced tumorigenesis.