The role of viral and host microRNAs in the Aujeszky's disease virus during the infection process

The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases

Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.

Host miRNA and mRNA profiles during in DEF and duck after DHAV-1 infection

DHAV-1 is a highly infectious pathogen that can cause acute hepatitis in ducklings. MicroRNA (miRNA) plays an essential regulatory role in virus response. We characterized and compared miRNA and mRNA expression profiles in duck embryonic fibroblasts (DEF) and the liver of ducklings infected with DHAV-1. DHAV-1 infected DEF was divided into infection group (D group) and blank group (M group), and DHAV-1 infected duckling group was divided into infection group (H group) and blank group (N group). D vs. M have 130 differentially expressed (DE) miRNA (DEM) and 2204 differentially expressed (DE) mRNA (DEG), H vs. N have 72 DEM and 1976 DEG. By the intersection of D vs. M and H vs. N comparisons, 15 upregulated DEM, 5 downregulated DEM, 340 upregulated DEG and 50 downregulated DEG were found with both in vivo and in vitro DHAV-1 infection. In particular, we identified the same DE miRNA target genes and functional annotations of DE mRNA. We enriched with multiple gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which may have important roles in viral virulence, host immunity, and metabolism. We selected miR-155, which is co-upregulated, and found that miR-155 targets SOCS1 to inhibit DHVA-1 replication.

Unravelling the impact of epigenetic mechanisms on offspring growth, production, reproduction and disease susceptibility

Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNA molecules, play a critical role in gene expression and regulation in livestock species, influencing development, reproduction and disease resistance. DNA methylation patterns silence gene expression by blocking transcription factor binding, while histone modifications alter chromatin structure and affect DNA accessibility. Livestock-specific histone modifications contribute to gene expression and genome stability. Non-coding RNAs, including miRNAs, piRNAs, siRNAs, snoRNAs, lncRNAs and circRNAs, regulate gene expression post-transcriptionally. Transgenerational epigenetic inheritance occurs in livestock, with environmental factors impacting epigenetic modifications and phenotypic traits across generations. Epigenetic regulation revealed significant effect on gene expression profiling that can be exploited for various targeted traits like muscle hypertrophy, puberty onset, growth, metabolism, disease resistance and milk production in livestock and poultry breeds. Epigenetic regulation of imprinted genes affects cattle growth and metabolism while epigenetic modifications play a role in disease resistance and mastitis in dairy cattle, as well as milk protein gene regulation during lactation. Nutri-epigenomics research also reveals the influence of maternal nutrition on offspring's epigenetic regulation of metabolic homeostasis in cattle, sheep, goat and poultry. Integrating cyto-genomics approaches enhances understanding of epigenetic mechanisms in livestock breeding, providing insights into chromosomal structure, rearrangements and their impact on gene regulation and phenotypic traits. This review presents potential research areas to enhance production potential and deepen our understanding of epigenetic changes in livestock, offering opportunities for genetic improvement, reproductive management, disease control and milk production in diverse livestock species.

Virus-Derived Small RNAs and microRNAs in Health and Disease

MicroRNAs (miRNAs) are short noncoding RNAs that can regulate all steps of gene expression (induction, transcription, and translation). Several virus families, primarily double-stranded DNA viruses, encode small RNAs (sRNAs), including miRNAs. These virus-derived miRNAs (v-miRNAs) help the virus evade the host's innate and adaptive immune system and maintain an environment of chronic latent infection. In this review, the functions of the sRNA-mediated virus-host interactions are highlighted, delineating their implication in chronic stress, inflammation, immunopathology, and disease. We provide insights into the latest viral RNA-based research-in silico approaches for functional characterization of v-miRNAs and other RNA types. The latest research can assist toward the identification of therapeutic targets to combat viral infections.

Expression Profiles and Interaction of MicroRNA and Transcripts in Response to Bovine Leukemia Virus Exposure

Bovine leukemia virus (BLV) infection in cattle is omnipresent, which causes significantly economical losses worldwide. The objective of this study was to determine microRNA (miRNA) and transcript profiles and to establish their relationship in response to exposure to the virus. Small noncoding and messenger RNA were extracted and sequenced from serum and white blood cells (WBCs) derived from seven BLV seropositive and seven seronegative cows. Transcriptomic profiles were generated by sequencing RNA libraries from WBC. Bta-miR-206 and bta-miR-133a-3p were differentially expressed in serum (P < 0.05). In WBC, bta-miR-335-3p, bta-miR-375, and bta-novel-miR76-3p were differentially expressed (P < 0.03). There were 64 differentially expressed transcripts (DETs). Gene ontology (GO) analysis of the DETs overexpressed in the seropositive group with GOs of response to stimulus and immune system process predicted that the DETs could potentially negatively regulate viral life cycle and viral entry or release from host cells. In addition, the DETs depleted in the seropositive group could play a role in the downregulation of antigen processing and presentation of endogenous peptide antigen via MHC class I. The differentially expressed miRNAs targeted 17 DETs, among which the expressions of bta-miR-133a-3p and bta-miR-335-3p were significantly negatively correlated with the expressions of ENSBTAT00000079143 and ENSBTAT00000066733, respectively. Under high prediction criteria, 90 targets of the differentially expressed miRNAs were all non-DETs. The most enriched biological process GO term of the targets was the RNA-dependent DNA biosynthetic process, which could be associated with virus replication. These results suggested that the differentially expressed miRNAs fine-tune most of the target genes in responding to BLV exposure. In addition, Bta-miR-206 interacted with BLV regulatory genes rex and tax by targeting their coding regions. A further study of the miRNAs and the genes may reveal the molecular mechanisms of BLV infection and uncover possible ways to prevent the infection.

The Role of Latency-Associated Transcripts in the Latent Infection of Pseudorabies Virus

Pseudorabies virus (PRV) can cause neurological, respiratory, and reproductive diseases in pigs and establish lifelong latent infection in the peripheral nervous system (PNS). Latent infection is a typical feature of PRV, which brings great difficulties to the prevention, control, and eradication of pseudorabies. The integral mechanism of latent infection is still unclear. Latency-associated transcripts (LAT) gene is the only transcriptional region during latent infection of PRV which plays the key role in regulating viral latent infection and inhibiting apoptosis. Here, we review the characteristics of PRV latent infection and the transcriptional characteristics of the LAT gene. We also analyzed the function of non-coding RNA (ncRNA) produced by the LAT gene and its importance in latent infection. Furthermore, we provided possible strategies to solve the problem of latent infection of virulent PRV strains in the host. In short, the detailed mechanism of PRV latent infection needs to be further studied and elucidated.

Functional Analysis of a Frontal miRNA Cluster Located in the Large Latency Transcript of Pseudorabies Virus

MicroRNAs (miRNAs) have been identified as a class of crucial regulators of virus-host crosstalk, modulating such processes as viral replication, antiviral immune response, viral latency, and pathogenesis. Pseudorabies virus (PRV), a model for the study of alphaherpesvirus biology, codes for 11 distinct miRNAs mapped to the ~4.6 kb intron of Large Latency Transcript (LLT). Recent studies have revealed the role of clusters consisting of nine and eleven miRNA genes in the replication and virulence of PRV. The function of separate miRNA species in regulating PRV biology has not been thoroughly investigated. To analyze the regulatory potential of three PRV miRNAs located in the frontal cluster of the LLT intron, we generated a research model based on the constitutive expression of viral miRNAs in swine testis cells (ST_LLT [1–3] cell line). Using a cell culture system providing a stable production of individual miRNAs at high levels, we demonstrated that the LLT [1–3] miRNA cluster significantly downregulated IE180, EP0, and gE at the early stages of PRV infection. It was further determined that LLT [1–3] miRNAs could regulate the infection process, leading to a slight distortion in transmission and proliferation ability. Collectively, our findings indicate the potential of LLT [1–3] miRNAs to retard the host responses by reducing viral antigenic load and suppressing the expansion of progeny viruses at the early stages of infection.

MicroRNA-206 inhibits influenza A virus replication by targeting tankyrase 2

Due to the frequent mutations, influenza A virus (IAV) becomes resistant to anti-viral drugs targeting influenza viral proteins. There are increasing interests in anti-viral agents that target host cellular proteins required for virus replication. Tankyrase (TNKS) has poly (ADP-ribose) polymerase activity and is a negative regulator of many host proteins. The objectives of this study are to study the role of TNKS2 in IAV infection, identify the microRNAs targeting TNKS2, and to understand the mechanisms involved. We found that TNKS2 expression was elevated in human lung epithelial cells and mouse lungs during IAV infection. Knock-down of TNKS2 by RNA interference reduced viral replication. Using a computation approach and 3'-untranslation regions (3'-UTR) reporter assay, we identified miR-206 as the microRNA that targeted TNKS2. Overexpression of miR-206 reduced viral protein levels and virus production in cell culture. The effect of miR-206 on IAV replication was strain-independent. miR-206 activated JNK/c-Jun signalling, induced type I interferon expression and enhanced Stat signalling. Finally, the delivery of an adenovirus expressing miR-206 into the lung of mice challenged with IAV increased type I interferon response, suppressed viral load in the lungs and increased survival. Our results indicate that miR-206 has anti-influenza activity by targeting TNKS2 and subsequently activating the anti-viral state.

Functional analysis of prv-miR-LLT11a encoded by pseudorabies virus

Viral-encoded microRNAs (miRNAs) have vital roles in the regulation of virus replications and host immune responses. The results of previous studies have indicated that miRNA clusters are involved in the replication and virulence of the pseudorabies virus (PRV), which may potentially lead to immune escape or facilitation of PRV replication. This study's previous research revealed that prv-miR-LLT11a was differentially expressed during PRV infection. The present study's results have demonstrated that prv-miR-LLT11a could significantly inhibit PRV replication. It was further determined that SLA-1 was the target gene of prv-miR-LLT11a, and simultaneously, that overexpression of prv-miR-LLT11a could downregulate the mRNA and protein levels of SLA-1 in a dose-independent manner. Furthermore, the present study also observed that prv-miR-LLT11a can downregulate TAP1 expression. Our findings provide a better understanding of the molecular mechanism involved in the effects of prv-miR-LLT11a on SLA-1 and TAP1 as well as its involvement in immune system evasion of PRV.

MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data

MicroRNA-offset RNAs (moRNAs) are microRNA-like small RNAs generated by microRNA precursors. To date, little is known about moRNAs and bioinformatics tools to inspect their expression are still missing. We developed miR&moRe2, the first bioinformatics method to consistently characterize microRNAs, moRNAs, and their isoforms from small RNA sequencing data. To illustrate miR&moRe2 discovery power, we applied it to several published datasets. MoRNAs identified by miR&moRe2 were in agreement with previous research findings. Moreover, we observed that moRNAs and new microRNAs predicted by miR&moRe2 were downregulated upon the silencing of the microRNA-biogenesis pathway. Further, in a sizeable dataset of human blood cell populations, tens of novel miRNAs and moRNAs were discovered, some of them with significantly varied expression levels among the cell types. Results demonstrate that miR&moRe2 is a valid tool for a comprehensive study of small RNAs generated from microRNA precursors and could help to investigate their biogenesis and function.

Cellular microRNA-155 Regulates Virus-Induced Inflammatory Response and Protects against Lethal West Nile Virus Infection

West Nile virus (WNV) is a flavivirus that has disseminated globally as a significant cause of viral encephalitis in humans. MircoRNA-155 (miR-155) regulates various aspects of innate and adaptive immune responses. We previously reported that WNV infection induces upregulation of miR-155 in mice brains. In the current study, we demonstrate the critical role of miR-155 in restricting the pathogenesis of WNV infection in mice. Compared to wild-type (WT) mice, miR-155 knockout mice exhibited significantly higher morbidity and mortality after infection with either a lethal strain, WNV NY99, or a non-lethal strain, WNV Eg101. Increased mortality in miR-155^−/− mice was associated with significantly high WNV burden in the serum and brains. Protein levels of interferon (IFN)-α in the serum and brains were higher in miR-155^−/− mice. However, miR-155^−/− mice exhibited significantly lower protein levels of anti-viral interleukin (IL)-1β, IL-12, IL-6, IL-15, and GM-CSF despite the high viral load. Primary mouse cells lacking miR-155 were more susceptible to infection with WNV compared to cells derived from WT mice. Besides, overexpression of miR-155 in human neuronal cells modulated anti-viral cytokine response and resulted in significantly lower WNV replication. These data collectively indicate that miR-155 restricts WNV production in mouse and human cells and protects against lethal WNV infection in mice.

African swine fever virus does not express viral microRNAs in experimentally infected pigs

Background

African swine fever virus (ASFV) is the etiological agent of African swine fever (ASF), a re-expanding devastating and highly lethal hemorrhagic viral disease. microRNAs (miRNAs) are a new class of small non-coding RNAs that regulate gene expression post-transcriptionally. The discovery of virus specific miRNAs has increased both in number and importance in the past few years. We have recently described the differential expression of several porcine miRNAs during in vivo infection with attenuated and virulent ASFV strains. Here, we have extended these studies trying to identify the presence of viral miRNAs encoded by ASFV in an in vivo infection in pigs.

Results

Sixteen small RNA libraries were analyzed from spleen and submandibular lymph nodes obtained from eight pigs, seven infected with either the virulent E75 ASFV strain or its attenuated counterpart E75CV1, or from pigs surviving E75CV1-infection and challenged with BA71 (heterologous challenge) and one non infected as negative control. Samples were recovered at different times post-infection. Libraries were analyzed by next-generation sequencing. Some viral miRNA candidates were initially identified, which did not correspond to porcine miRNAs. Further structural analyses were carried out in order to confirm if they met the conformational requirements to be considered a viral miRNA.

Conclusions

The analysis of sixteen small RNA libraries prepared from two different tissues obtained from pigs experimentally infected with E75, E75CV1 or with E75CV1 plus BA71, revealed the presence of six potential miRNA sequences but none of them met the requirements to be considered as viral miRNAs. Thus, we can conclude that ASFV does not express miRNAs in vivo, at least under the experimental conditions described here.

MicroRNAs and cancer: Key paradigms in molecular therapy

MicroRNAs (miRNAs) are a type of small non-coding RNA molecule that performs an important role in post-transcriptional gene regulation. Since miRNAs were first identified in 1993, a number of studies have demonstrated that they act as tumor suppressors or oncogenes in human cancer, including colorectal, lung, brain, breast and liver cancer, and leukemia. Large high-throughput studies have previously revealed that miRNA profiling is critical for the diagnosis and prognosis of patients with cancer, while certain miRNAs possess the potential to be used as diagnostic and prognostic biomarkers or therapeutic targets in cancer. The present study reviews the studies and examines the roles of miRNAs in cancer diagnosis, prognosis and treatment, and discusses the potential therapeutic modality of exploiting miRNAs.

Differential expression of porcine microRNAs in African swine fever virus infected pigs: a proof-of-concept study

BACKGROUND

African swine fever (ASF) is a re-expanding devastating viral disease currently threatening the pig industry worldwide. MicroRNAs are a class of 17-25 nucleotide non- coding RNAs that have been shown to have critical functions in a wide variety of biological processes, such as cell differentiation, cell cycle regulation, carcinogenesis, apoptosis, regulation of immunity as well as in viral infections by cleavage or translational repression of mRNAs. Nevertheless, there is no information about miRNA expression in an ASFV infection.

METHODS

In this proof-of-concept study, we have analyzed miRNAs expressed in spleen and submandibular lymph node of experimentally infected pigs with a virulent (E75) or its derived attenuated (E75CV1) ASFV strain, as well as, at different times post-infection with the virulent strain, by high throughput sequencing of small RNA libraries.

RESULTS

Spleen presented a more differential expression pattern than lymph nodes in an ASFV infection. Of the most abundant miRNAs, 12 were differentially expressed in both tissues at two different times in infected animals with the virulent strain. Of these, miR-451, miR-145-5p, miR-181a and miR-122 presented up-regulation at late times post-infection while miR-92a, miR-23a, miR-92b-3p, miR-126-5p, miR-126-3p, miR-30d, miR-23b and miR-92c showed down-regulation. Of the 8 differentially expressed miRNAs identified at the same time post-infection in infected animals with the virulent strain compared with animals infected with its attenuated strain, miR-126-5p, miR-92c, miR-92a, miR-30e-5p and miR-500a-5p presented up-regulation whereas miR-125b, miR-451 and miR-125a were down-regulated. All these miRNAs have been shown to be associated with cellular genes involved in pathways related to the immune response, virus-host interactions as well as with several viral genes.

CONCLUSION

The study of miRNA expression will contribute to a better understanding of African swine fever virus pathogenesis, essential in the development of any disease control strategy.

MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection

Pseudorabies virus (PRV), an alpha herpesvirus can enter the mammalian nervous system, causing Aujezsky's disease. Previous studies have reported an alteration of microRNA (miRNA) expression levels during PRV infections. However, knowledge regarding miRNA response in nervous cells to PRV infection is still unknown. To address this issue, small RNA libraries from infected and uninfected mouse neuroblastoma cells were assessed after Illumina deep sequencing. A total of eight viral miRNA were identified, and ten host miRNAs showed significantly different expression upon PRV infection. Among these, five were analyzed by stem-loop RT-qPCR, which confirmed the above data. Interestingly, these viral miRNAs were mainly found in the large latency transcript region of PRV, and predicted to target a variety of genes, forming a complicated regulatory network. Moreover, ten cellular miRNAs were expressed differently upon PRV infection, including nine upregulated and one downregulated miRNAs. Host targets of these miRNAs obtained by bioinformatics analysis belonged to large signaling networks, mainly encompassing calcium signaling pathway, cAMP signaling pathway, MAPK signaling pathway, and other nervous-associated pathways. These findings further highlighted miRNA features in nervous cells after PRV infection and contributed to unveil the underlying mechanisms of neurotropism as well as the neuropathogenesis of PRV.

Evolutionary Diversity of Suid Herpesvirus 1 Based on Ul44 Partial Sequences

OBJECTIVE

The aim of this study was to use partial Ul44 sequences (glycoprotein C) of Suid herpesvirus 1 to examine the evolution and dynamics of the virus in different periods and hosts.

METHODS

Phylogenetic trees were constructed using the software MrBayes after analysis in the software jModelTest to evaluate the best phylogenetic models. The software SplitsTree 4.0 was used to create phylogenetic networks, and the BEAST program was used to generate data on phylogeography. Replication kinetics and serum neutralization tests were applied to tree strains from different phylogenetic groups.

RESULTS

Ul44 sequences derived from domestic swine and wild swine clustered in different clades and had different selective pressures depending on the host. We found no differences in replication kinetics and serum neutralization tests in the strains tested. Data show that the evolution of herpesviruses is complex, and different genetic groups may be evolving at different rates. Ul44 is an important marker for molecular evolution and epidemiology studies, but it is not useful for biological information.

Identification and Analysis of Novel Viral and Host Dysregulated MicroRNAs in Variant Pseudorabies Virus-Infected PK15 Cells

Pseudorabies (PR) is one of the most devastating diseases in the pig industry. To identify changes in microRNA (miRNA) expression and post-transcriptional regulatory responses to PRV infection in porcine kidney epithelial (PK15) cells, we sequenced a small RNA (sRNA) library prepared from infected PK15 cells and compared it to a library prepared from uninfected cells using Illumina deep sequencing. Here we found 25 novel viral miRNAs by high-throughput sequencing and 20 of these miRNAs were confirmed through stem-loop RT-qPCR. Intriguingly, unlike the usual miRNAs encoded by the α-herpesviruses, which are found clustered in the large latency transcript (LLT), these novel viral miRNAs are throughout the PRV genome like β-herpesviruses. Viral miRNAs are predicted to target multiple genes and form a complex regulatory network. GO analysis on host targets of viral miRNAs were involved in complex cellular processes, including the metabolic pathway, biological regulation, stimulus response, signaling process and immune response. Moreover, 13 host miRNAs were expressed with significant difference after infection with PRV: 8 miRNAs were up-regulated and 5 miRNAs were down-regulated, which may affect viral replication in host cell. Our results provided new insight into the characteristic of miRNAs in response to PRV infection, which is significant for further study of these miRNAs function.

MicroRNAs Expressed during Viral Infection: Biomarker Potential and Therapeutic Considerations

MicroRNAs (miRNAs) are short sequences of noncoding single-stranded RNAs that exhibit inhibitory effects on complementary target mRNAs. Recently, it has been discovered that certain viruses express their own miRNAs, while other viruses activate the transcription of cellular miRNAs for their own benefit. This review summarizes the viral and/or cellular miRNAs that are transcribed during infection, with a focus on the biomarker and therapeutic potential of miRNAs (or their antagomirs). Several human viruses of clinical importance are discussed, namely, herpesviruses, polyomaviruses, hepatitis B virus, hepatitis C virus, human papillomavirus, and human immunodeficiency virus.

Evaluation of the capability of the PCV2 genome to encode miRNAs: lack of viral miRNA expression in an experimental infection

Porcine circovirus type 2 (PCV2) is a ssDNA virus causing PCV2-systemic disease (PCV2-SD), one of the most important diseases in swine. MicroRNAs (miRNAs) are a new class of small non-coding RNAs that regulate gene expression post-transcriptionally. Viral miRNAs have recently been described and the number of viral miRNAs has been increasing in the past few years. In this study, small RNA libraries were constructed from two tissues of subclinically PCV2 infected pigs to explore if PCV2 can encode viral miRNAs. The deep sequencing data revealed that PCV2 does not express miRNAs in an in vivo subclinical infection.

Identification of microRNAs in PCV2 subclinically infected pigs by high throughput sequencing

Porcine circovirus type 2 (PCV2) is the essential etiological infectious agent of PCV2-systemic disease and has been associated with other swine diseases, all of them collectively known as porcine circovirus diseases. MicroRNAs (miRNAs) are a new class of small non-coding RNAs that regulate gene expression post-transcriptionally. miRNAs play an increasing role in many biological processes. The study of miRNA-mediated host-pathogen interactions has emerged in the last decade due to the important role that miRNAs play in antiviral defense. The objective of this study was to identify the miRNA expression pattern in PCV2 subclinically infected and non-infected pigs. For this purpose an experimental PCV2 infection was carried out and small-RNA libraries were constructed from tonsil and mediastinal lymph node (MLN) of infected and non-infected pigs. High throughput sequencing determined differences in miRNA expression in MLN between infected and non-infected while, in tonsil, a very conserved pattern was observed. In MLN, miRNA 126-3p, miRNA 126-5p, let-7d-3p, mir-129a and mir-let-7b-3p were up-regulated whereas mir-193a-5p, mir-574-5p and mir-34a down-regulated. Prediction of functional analysis showed that these miRNAs can be involved in pathways related to immune system and in processes related to the pathogenesis of PCV2, although functional assays are needed to support these predictions. This is the first study on miRNA gene expression in pigs infected with PCV2 using a high throughput sequencing approach in which several host miRNAs were differentially expressed in response to PCV2 infection.

Current transcriptomics in pig immunity research

Swine performance in the face of disease challenge is becoming progressively more important. To improve the pig’s robustness and resilience against pathogens through selection, a better understanding of the genetic and epigenetic factors in the immune response is required. This review highlights results from the most recent transcriptome research, and the meta-analyses performed, in the context of pig immunity. A technological overview is given including wholegenome microarrays, immune-specific arrays, small-scale high-throughput expression methods, high-density tiling arrays, and next generation sequencing (NGS). Although whole genome microarray techniques will remain complementary to NGS for some time in domestic species, research will transition to sequencing-based methods due to cost-effectiveness and the extra information that such methods provide. Furthermore, upcoming high-throughput epigenomic studies, which will add greatly to our knowledge concerning the impact of epigenetic modifications on pig immune response, are listed in this review. With emphasis on the insights obtained from transcriptomic analyses for porcine immunity, we also discuss the experimental design in pig immunity research and the value of the newly published porcine genome assembly in using the pig as a model for human immune response. We conclude by discussing the importance of establishing community standards to maximize the possibility of integrative computational analyses, such as was clearly beneficial for the human ENCODE project.

A 2.5-kilobase deletion containing a cluster of nine microRNAs in the latency-associated-transcript locus of the pseudorabies virus affects the host response of porcine trigeminal ganglia during established latency

The alphaherpesvirus pseudorabies virus (PrV) establishes latency primarily in neurons of trigeminal ganglia when only the transcription of the latency-associated transcript (LAT) locus is detected. Eleven microRNAs (miRNAs) cluster within the LAT, suggesting a role in establishment and/or maintenance of latency. We generated a mutant (M) PrV deleted of nine miRNA genes which displayed properties that were almost identical to those of the parental PrV wild type (WT) during propagation in vitro. Fifteen pigs were experimentally infected with either WT or M virus or were mock infected. Similar levels of virus excretion and host antibody response were observed in all infected animals. At 62 days postinfection, trigeminal ganglia were excised and profiled by deep sequencing and quantitative RT-PCR. Latency was established in all infected animals without evidence of viral reactivation, demonstrating that miRNAs are not essential for this process. Lower levels of the large latency transcript (LLT) were found in ganglia infected by M PrV than in those infected by WT PrV. All PrV miRNAs were expressed, with highest expression observed for prv-miR-LLT1, prv-miR-LLT2 (in WT ganglia), and prv-miR-LLT10 (in both WT and M ganglia). No evidence of differentially expressed porcine miRNAs was found. Fifty-four porcine genes were differentially expressed between WT, M, and control ganglia. Both viruses triggered a strong host immune response, but in M ganglia gene upregulation was prevalent. Pathway analyses indicated that several biofunctions, including those related to cell-mediated immune response and the migration of dendritic cells, were impaired in M ganglia. These findings are consistent with a function of the LAT locus in the modulation of host response for maintaining a latent state.

IMPORTANCE

This study provides a thorough reference on the establishment of latency by PrV in its natural host, the pig. Our results corroborate the evidence obtained from the study of several LAT mutants of other alphaherpesviruses encoding miRNAs from their LAT regions. Neither PrV miRNA expression nor high LLT expression levels are essential to achieve latency in trigeminal ganglia. Once latency is established by PrV, the only remarkable differences are found in the pattern of host response. This indicates that, as in herpes simplex virus, LAT functions as an immune evasion locus.