Differential expression of genes encoding CD30L and P-selectin in cattle with Johne's disease: Progress toward a diagnostic gene expression signature

Differential gene expression in peripheral leukocytes of pre-weaned Holstein heifer calves with respiratory disease

Bovine respiratory disease (BRD) is a leading cause of calf morbidity and mortality, and prevalence remains high despite current management practices. Differential gene expression (DGE) provides detailed insight into individual immune responses and can illuminate enriched pathways and biomarkers that contribute to disease susceptibility and outcomes. The aims of this study were to investigate differences in peripheral leukocyte gene expression in Holstein preweaned heifer calves 1) with and without BRD, and 2) across weeks of age. Calves were enrolled for this short-term longitudinal study on two commercial dairies in Washington State. Calves were assessed every two weeks throughout the pre-weaning period using clinical respiratory scoring (CRS) and thoracic ultrasonography (TUS), and blood samples were collected. Calves were selected that were either healthy (n = 10) or had BRD diagnosed by CRS (n = 7), TUS (n = 6), or both (n = 6) in weeks 5 or 7 of life). Three consecutive time point samples were analyzed for each BRD calf consisting of PRE, ONSET, and POST samples. Nineteen genes of interest were selected based on previous gene expression studies in cattle: ALOX15, BPI, CATHL6, CXCL8, DHX58, GZMB, HPGD, IFNG, IL17D, IL1R2, ISG15, LCN2, LIF, MX1, OAS2, PGLYRP1, S100A8, SELP, and TNF. Comparisons were made between age and disease time point matched BRD and healthy calves as well as between calf weeks of age. No DGE was observed between diseased and healthy calves; however, DGE was observed between calf weeks of age regardless of disease state. Developmental differences in leukocyte gene expression, phenotype, and functionality make pre-weaned calves immunologically distinct from mature cattle, and early life shifts in calf leukocyte populations likely contribute to the age-related gene expression differences we observed. Age overshadows disease impacts to influence gene expression in young calves, and immune development progresses upon a common trajectory regardless of disease during the preweaning period.

Johne's Disease in Dairy Cattle: An Immunogenetic Perspective

Johne's disease (JD), also known as paratuberculosis, is a severe production-limiting disease with significant economic and welfare implications for the global cattle industry. Caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP), JD manifests as chronic enteritis in infected cattle. In addition to the economic losses and animal welfare issues associated with JD, MAP has attracted public health concerns with potential association with Crohn's disease, a human inflammatory bowel disease. The lack of effective treatment options, such as a vaccine, has hampered JD control resulting in its increasing global prevalence. The disease was first reported in 1895, but in recognition of its growing economic impact, extensive recent research facilitated by a revolution in technological approaches has led to significantly enhanced understanding of the immunological, genetic, and pathogen factors influencing disease pathogenesis. This knowledge has been derived from a variety of diverse models to elucidate host-pathogen interactions including in vivo and in vitro experimental infection models, studies measuring immune parameters in naturally-infected animals, and by studies conducted at the population level to enable the estimation of genetic parameters, and the identification of genetic markers and quantitative trait loci (QTL) putatively associated with susceptibility or resistance to JD. The main objectives of this review are to summarize these recent developments from an immunogenetics perspective and attempt to extract the principal and common findings emerging from this wealth of recent information. Based on these analyses, and in light of emerging technologies such as gene-editing, we conclude by discussing potential future avenues for effectively mitigating JD in cattle.

Serum Metabolomic Profiles of Paratuberculosis Infected and Infectious Dairy Cattle by Ambient Mass Spectrometry

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of paratuberculosis [Johne's disease (JD)], a chronic disease that causes substantial economic losses in the dairy cattle industry. The long incubation period means clinical signs are visible in animals only after years, and some cases remain undetected because of the subclinical manifestation of the disease. Considering the complexity of JD pathogenesis, animals can be classified as infected, infectious, or affected. The major limitation of currently available diagnostic tests is their failure in detecting infected non-infectious animals. The present study aimed to identify metabolic markers associated with infected and infectious stages of JD. Direct analysis in real time coupled with high resolution mass spectrometry (DART-HRMS) was, hence, applied in a prospective study where cohorts of heifers and cows were followed up annually for 2–4 years. The animals' infectious status was assigned based on a positive result of both serum ELISA and fecal PCR, or culture. The same animals were retrospectively assigned to the status of infected at the previous sampling for which all JD tests were negative. Stored sera from 10 infected animals and 17 infectious animals were compared with sera from 20 negative animals from the same herds. Two extraction protocols and two (-/+) ionization modes were tested. The three most informative datasets out of the four were merged by a mid-level data fusion approach and submitted to partial least squares discriminant analysis (PLS-DA). Compared to the MAP negative subjects, metabolomic analysis revealed the m/z signals of isobutyrate, dimethylethanolamine, palmitic acid, and rhamnitol were more intense in infected animals. Both infected and infectious animals showed higher relative intensities of tryptamine and creatine/creatinine as well as lower relative abundances of urea, glutamic acid and/or pyroglutamic acid. These metabolic differences could indicate altered fat metabolism and reduced energy intake in both infected and infectious cattle. In conclusion, DART-HRMS coupled to a mid-level data fusion approach allowed the molecular features that identified preclinical stages of JD to be teased out.

Application of Transcriptomics to Enhance Early Diagnostics of Mycobacterial Infections, with an Emphasis on Mycobacterium avium ssp. paratuberculosis

Mycobacteria cause a wide variety of disease in human and animals. Species that infect ruminants include M. bovis and M. avium ssp. paratuberculosis (MAP). MAP is the causative agent of Johne’s disease in ruminants, which is a chronic granulomatous enteric infection that leads to severe economic losses worldwide. Characteristic of MAP infection is the long, latent phase in which intermittent shedding can take place, while diagnostic tests are unable to reliably detect an infection in this stage. This leads to unnoticed dissemination within herds and the presence of many undetected, silent carriers, which makes the eradication of Johne’s disease difficult. To improve the control of MAP infection, research is aimed at improving early diagnosis. Transcriptomic approaches can be applied to characterize host-pathogen interactions during infection, and to develop novel biomarkers using transcriptional profiles. Studies have focused on the identification of specific RNAs that are expressed in different infection stages, which will assist in the development and clinical implementation of early diagnostic tests.

Biomarker Discovery in Animal Health and Disease: The Application of Post-Genomic Technologies

The causes of many important diseases in animals are complex and multifactorial, which present unique challenges. Biomarkers indicate the presence or extent of a biological process, which is directly linked to the clinical manifestations and outcome of a particular disease. Identifying biomarkers or biomarker profiles will be an important step towards disease characterization and management of disease in animals. The emergence of post-genomic technologies has led to the development of strategies aimed at identifying specific and sensitive biomarkers from the thousands of molecules present in a tissue or biological fluid. This review will summarize the current developments in biomarker discovery and will focus on the role of transcriptomics, proteomics and metabolomics in biomarker discovery for animal health and disease.

Knowledge gaps that hamper prevention and control of Mycobacterium avium subspecies paratuberculosis infection

In the last decades, many regional and country-wide control programmes for Johne's disease (JD) were developed due to associated economic losses, or because of a possible association with Crohn's disease. These control programmes were often not successful, partly because management protocols were not followed, including the introduction of infected replacement cattle, because tests to identify infected animals were unreliable, and uptake by farmers was not high enough because of a perceived low return on investment. In the absence of a cure or effective commercial vaccines, control of JD is currently primarily based on herd management strategies to avoid infection of cattle and restrict within-farm and farm-to-farm transmission. Although JD control programmes have been implemented in most developed countries, lessons learned from JD prevention and control programmes are underreported. Also, JD control programmes are typically evaluated in a limited number of herds and the duration of the study is less than 5 year, making it difficult to adequately assess the efficacy of control programmes. In this manuscript, we identify the most important gaps in knowledge hampering JD prevention and control programmes, including vaccination and diagnostics. Secondly, we discuss directions that research should take to address those knowledge gaps.

Potential application of emerging diagnostic techniques to the diagnosis of bovine Johne's disease (paratuberculosis)

Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne's disease (paratuberculosis), a chronic wasting disease in cattle with important welfare, economic and potential public health implications. Current tests are unable to recognise all stages of the disease, which makes it difficult to diagnose and control. This review explores emerging diagnostic techniques that could complement and enhance the diagnosis of MAP infection, including bacteriophage analysis, new MAP-specific antigens, host protein expression in response to infection, transcriptomic studies, analysis of microRNAs and investigation of the gastrointestinal microbiome. It emphasises the inherent challenges of diagnosing bovine Johne's disease and investigates novel areas which may have the potential both to advance our understanding of the immunopathology of MAP infection and to augment current diagnostic tests.

Susceptibility to and diagnosis of Mycobacterium avium subspecies paratuberculosis infection in dairy calves: A review

The primary objectives of paratuberculosis control programs are reducing exposure of calves to Mycobacterium avium subspecies paratuberculosis (MAP), reducing herd infection pressure and regular testing of cattle >36 months of age. Although control programs based on these principles have reduced prevalence of MAP infection in dairy herds, they have generally not eliminated the infection. Recent infection trial(s) have yielded new knowledge regarding diagnostic testing and age- and dose-dependent susceptibility to MAP infection. Calves up to 1 year of age are still susceptible to MAP infection; therefore, control programs should refrain from referring to specific ages with respect to susceptibility and prevention of new infections. Notwithstanding, lesions were more severe when calves were inoculated at 2 weeks versus 1 year of age. Furthermore, a high inoculation dose resulted in more pronounced lesions than a low inoculation dose, especially in young calves. Consequently, keeping infection pressure low should decrease the incidence of new MAP infections and severity of JD in cattle that do acquire the infection. It was also evident that early diagnosis of MAP infection was possible and could improve efficacy of control programs. Although its use will still need to be validated in the field, a combination of antibody ELISA and fecal culture in young stock, in addition to testing cattle >36 months of age when screening a herd for paratuberculosis, was expected to improve detection of dairy cattle infected with MAP. Although calves were inoculated using a standardized method in a controlled environment, there were substantial differences among calves with regards to immune response, shedding and pathology. Therefore, we inferred there were genetic differences in susceptibility. Important insights were derived from experimental infection trials. Therefore, it was expected that these could improve paratuberculosis control programs by reducing severity and incidence of JD by lowering infection pressure on-farm, and reducing exposure of young calves and older cattle. Furthermore, an earlier diagnosis could be achieved by combining ELISA and fecal shedding in young stock, in addition to testing cattle >36 months of age.

Metabolomic profiling in cattle experimentally infected with Mycobacterium avium subsp. paratuberculosis

The sensitivity of current diagnostics for Johne's disease, a slow, progressing enteritis in ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP), is too low to reliably detect all infected animals in the subclinical stage. The objective was to identify individual metabolites or metabolite profiles that could be used as biomarkers of early MAP infection in ruminants. In a monthly follow-up for 17 months, calves infected at 2 weeks of age were compared with aged-matched controls. Sera from all animals were analyzed by 1H nuclear magnetic resonance spectrometry. Spectra were acquired, processed, and quantified for analysis. The concentration of many metabolites changed over time in all calves, but some metabolites only changed over time in either infected or non-infected groups and the change in others was impacted by the infection. Hierarchical multivariate statistical analysis achieved best separation between groups between 300 and 400 days after infection. Therefore, a cross-sectional comparison between 1-year-old calves experimentally infected at various ages with either a high- or a low-dose and age-matched non-infected controls was performed. Orthogonal Projection to Latent Structures Discriminant Analysis (OPLS DA) yielded distinct separation of non-infected from infected cattle, regardless of dose and time (3, 6, 9 or 12 months) after infection. Receiver Operating Curves demonstrated that constructed models were high quality. Increased isobutyrate in the infected cattle was the most important agreement between the longitudinal and cross-sectional analysis. In general, high- and low-dose cattle responded similarly to infection. Differences in acetone, citrate, glycerol and iso-butyrate concentrations indicated energy shortages and increased fat metabolism in infected cattle, whereas changes in urea and several amino acids (AA), including the branched chain AA, indicated increased protein turnover. In conclusion, metabolomics was a sensitive method for detecting MAP infection much sooner than with current diagnostic methods, with individual metabolites significantly distinguishing infected from non-infected cattle.

Veterinary and human biobanking practices: enhancing molecular sample integrity

Animal models have historically informed veterinary and human pathophysiology. Next-generation genomic sequencing and molecular analyses using analytes derived from tissue require integrative approaches to determine macroanalyte integrity as well as morphology for imaging algorithms that can extend translational applications. The field of biospecimen science and biobanking will play critical roles in tissue sample collection and processing to ensure the integrity of macromolecules, aid experimental design, and provide more accurate and reproducible downstream genomic data. Herein, we employ animal experiments to combine protein expression analysis by microscopy with RNA integrity number and quantitative measures of morphologic changes of autolysis. These analyses can be used to predict the effect of preanalytic variables and provide the basis for standardized methods in tissue sample collection and processing. We also discuss the application of digital imaging with quantitative RNA and tissue-based protein measurements to show that genomic methods augment traditional in vivo imaging to support biospecimen science. To make these observations, we have established a time course experiment of murine kidney tissues that predicts conventional measures of RNA integrity by RIN analysis and provides reliable and accurate measures of biospecimen integrity and fitness, in particular for time points less than 3 hours post-tissue resection.

Differential gene expression segregates cattle confirmed positive for bovine tuberculosis from antemortem tuberculosis test-false positive cattle originating from herds free of bovine tuberculosis

Antemortem tests for bovine tuberculosis (bTB) currently used in the US measure cell-mediated immune responses against Mycobacterium bovis. Postmortem tests for bTB rely on observation of gross and histologic lesions of bTB, followed by bacterial isolation or molecular diagnostics. Cumulative data from the state of Michigan indicates that 98 to 99% of cattle that react positively in antemortem tests are not confirmed positive for bTB at postmortem examination. Understanding the fundamental differences in gene regulation between antemortem test-false positive cattle and cattle that have bTB may allow identification of molecular markers that can be exploited to better separate infected from noninfected cattle. An immunospecific cDNA microarray was used to identify altered gene expression (P ≤ 0.01) of 122 gene features between antemortem test-false positive cattle and bTB-infected cattle following a 4-hour stimulation of whole blood with tuberculin. Further analysis using quantitative real-time PCR assays validated altered expression of 8 genes that had differential power (adj  P ≤ 0.05) to segregate cattle confirmed positive for bovine tuberculosis from antemortem tuberculosis test-false positive cattle originating from herds free of bovine tuberculosis.

Tuberculosis immunity: opportunities from studies with cattle

Mycobacterium tuberculosis and M. bovis share >99% genetic identity and induce similar host responses and disease profiles upon infection. There is a rich history of codiscovery in the development of control measures applicable to both human and bovine tuberculosis (TB) including skin-testing procedures, M. bovis BCG vaccination, and interferon-γ release assays. The calf TB infection model offers several opportunities to further our understanding of TB immunopathogenesis. Recent observations include correlation of central memory immune responses with TB vaccine efficacy, association of SIRPα⁺ cells in ESAT-6:CFP10-elicited multinucleate giant cell formation, early γδ T cell responses to TB, antimycobacterial activity of memory CD4⁺ T cells via granulysin production, association of specific antibody with antigen burden, and suppression of innate immune gene expression in infected animals. Partnerships teaming researchers with veterinary and medical perspectives will continue to provide mutual benefit to TB research in man and animals.

Genomic and transcriptomic studies in Mycobacterium avium subspecies paratuberculosis

Microarray technology is an important tool in functional genomic research. It has enabled a deeper analysis of genomic diversity among bacteria belonging to the Mycobacterium avium complex (MAC). In addition, the expression of thousands of genes can be studied simultaneously in a single experiment. With the complete genome sequence of a bovine isolate of M. avium subspecies paratuberculosis, and the independent construction of DNA microarrays in our laboratories, transcriptomic studies for this veterinary pathogen are now possible. Furthermore, the bovine genome sequence project is completed and bovine arrays have been developed to examine host responses to infection with M. avium subsp. paratuberculosis. Collectively, genomic and transcriptomic data has yielded novel insights surrounding the genetic regulation and biology of Johne's disease.

Gene expression profiling of PBMCs from Holstein and Jersey cows sub-clinically infected with Mycobacterium avium ssp. paratuberculosis

Infection of calves with intracellular Mycobacterium avium ssp. paratuberculosis (MAP) commonly results in a granulomatous, chronic inflammatory bowel disease known as Johne's disease. The asymptomatic stage of this infection can persist for the entire production life of an adult cow, resulting in reduced performance and premature culling, as well as transmission of MAP to progeny and herd-mates. It has been previously shown that the gene expression profiles of peripheral blood mononuclear cells (PBMCs) of healthy cows, and those chronically infected with MAP are inherently different, and that these changes may be indicative of disease progression. Since resistance to MAP infection is a heritable trait, and has been proposed to differ amongst domestic dairy cattle breeds, the objective of the present study was to compare gene expression profiles of PBMCs from healthy adult Holstein and Jersey cows to those considered to be sub-clinically infected with MAP, as indicated by serum ELISA. Microarray analysis using a platform containing more than 10,000 probes and ontological analysis identified differences in gene expression between a) healthy and infected cows, including genes involved in the inflammatory response, and calcium binding, and b) infected Holsteins and Jerseys, including genes involved in the immune response, and antigen processing and presentation. These results suggest a mixed pro- and anti-inflammatory phenotype of PBMCs from MAP-infected as compared to healthy control animals, and inherently different levels of immune and inflammatory-related gene expression between MAP-infected Holsteins and Jerseys.

Gene expression profiling of the host response to Mycobacterium bovis infection in cattle

Bovine tuberculosis (BTB), caused by Mycobacterium bovis, continues to pose a threat to livestock worldwide and, as a zoonotic infection, also has serious implications for human health. The implementation of comprehensive surveillance programmes to detect BTB has been successful in reducing the incidence of infection in many countries, yet BTB has remained recalcitrant to eradication in several EU states, particularly in Ireland and the UK. There are well-recognized limitations in the use of the current diagnostics to detect all infected animals and this has led to renewed efforts to uncover novel diagnostic biomarkers that may serve to enhance the performance of the tests. Studies of single immunological parameters have so far been unable to unlock the complexities of the immune response to mycobacterial infection. However, the development of high-throughput methods including pan-genomic gene expression technologies such as DNA microarrays has facilitated the simultaneous identification and analysis of thousands of genes and their interactions during the immune response. In addition, the application of these new genomic technologies to BTB has identified pathogen-associated immune response signatures of host infection. The objective of these investigations is to understand the changing profile of immune responses throughout the course of infection and to identify biomarkers for sensitive diagnosis, particularly during the early stages of infection. Transcriptional profiling via microarray and more recently via next-generation sequencing technologies may lead to the development of specific and sensitive diagnostics for M. bovis infection and will enhance the prospect of eradication of tuberculosis from cattle populations.

Oligonucleotide microarray technology and its application to Mycobacterium avium subsp. paratuberculosis research: a review

Microarrays represent a modern powerful technology, which have potential applications in many areas of biological research and provide new insights into the genomics and transcriptomics of living systems. The aim of this review is to describe the application of microarray technology for Mycobacterium avium subsp. paratuberculosis (MAP) research. The main focus points include a summary of results obtained for MAP using microarrays, examination of the fields of MAP research which are currently being investigated and possible areas of future research. This article is divided into two parts according to the type of nucleic acid used for array hybridisation. Articles related to MAP research using microarray technology are then divided according to the field of study, such as comparative genome analysis, diagnostics, expression or environmental studies.

Review Paper: Gene Expression Profiling in Veterinary and Human Medicine: Overview of Applications and Proposed Quality Control Practices

High throughput molecular analysis of veterinary tissue samples is being applied to a wide range of research questions aimed at improving survival, development of diagnostic assays, and improving the economics of commercial production of animal products. Many of these efforts also, implicitly or explicitly, have ramifications for the clinical care of humans and, potentially, animals. Here we provide an overview of applications of gene expression profiling in veterinary research and practice. We then focus on the current state of quality control and quality assurance efforts in gene expression profiling studies, underscoring lessons learned from such analysis of human samples. Finally, we propose practices aimed at ensuring the reliability and reproducibility of such assays. The implementation of quality assurance practices by a trained pathologist is an essential link in the chain of events leading ultimately to reliable and reproducible research findings and appropriate clinical care.

Innate gene repression associated with Mycobacterium bovis infection in cattle: toward a gene signature of disease

Background

Bovine tuberculosis is an enduring disease of cattle that has significant repercussions for human health. The advent of high-throughput functional genomics technologies has facilitated large-scale analyses of the immune response to this disease that may ultimately lead to novel diagnostics and therapeutic targets. Analysis of mRNA abundance in peripheral blood mononuclear cells (PBMC) from six Mycobacterium bovis infected cattle and six non-infected controls was performed. A targeted immunospecific bovine cDNA microarray with duplicated spot features representing 1,391 genes was used to test the hypothesis that a distinct gene expression profile may exist in M. bovis infected animals in vivo.

Results

In total, 378 gene features were differentially expressed at the P ≤ 0.05 level in bovine tuberculosis (BTB)-infected and control animals, of which 244 were expressed at lower levels (65%) in the infected group. Lower relative expression of key innate immune genes, including the Toll-like receptor 2 (TLR2) and TLR4 genes, lack of differential expression of indicator adaptive immune gene transcripts (IFNG, IL2, IL4), and lower BOLA major histocompatibility complex – class I (BOLA) and class II (BOLA-DRA) gene expression was consistent with innate immune gene repression in the BTB-infected animals. Supervised hierarchical cluster analysis and class prediction validation identified a panel of 15 genes predictive of disease status and selected gene transcripts were validated (n = 8 per group) by real time quantitative reverse transcription PCR.

Conclusion

These results suggest that large-scale expression profiling can identify gene signatures of disease in peripheral blood that can be used to classify animals on the basis of in vivo infection, in the absence of exogenous antigenic stimulation.

Validation of putative reference genes for qRT-PCR normalization in tissues and blood from pigs infected with Actinobacillus pleuropneumoniae

The quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) is a sensitive and very efficient technique for quantification of gene expression. However, qRT-PCR relies on accurate normalization of gene expression data, as RNA recovery and cDNA synthesis efficiency might vary from sample to sample. In the present study, six putative reference genes were validated for normalization of gene expression in three different tissues and in white blood cells from pigs experimentally infected with the common respiratory pathogen Actinobacillus pleuropneumoniae. Two dedicated validation programs (geNorm and Normfinder) were used to rank the six reference genes from best to worst. qRT-PCR data for the proinflammatory cytokine IL-6 was normalized using the proposed genes from geNorm and Normfinder as well as the commonly used reference gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH). IL-6 expression was quantified in white blood cells, liver, lymph nodes and tonsils from 10 infected pigs and 5 control pigs. After normalization using either geNorm or Normfinder IL-6 was shown to be significantly up-regulated (P<0.05) in all of the tissues from infected animals compared to non-infected control animals with a good agreement of expression differences between the two programs. On the contrary, normalization of IL-6 expression data from blood using GAPDH rendered the difference between infected and non-infected groups non-significant, and resulted in significantly different values compared to geNorm (P=0.01). Based on these results, we recommend to validate putative reference genes before normalization.