Genetic and Epigenetic Regulation of Immune Response and Resistance to Infectious Diseases in Domestic Ruminants

Blood and colostral IgM and IgG B cell repertoires in high, average, and low immune responder Holstein Friesian cows and heifers

In dairy cattle, genetic selection for higher antibody-mediated (AMIR) and cell-mediated (CMIR) immune responses can enhance disease resistance. Cattle produce a unique subset of B cells with B cell receptors with ultralong complementarity determining regions 3 (CDR3). Antibodies with these specialized structures have superior virus neutralization characteristics. Published studies of B cell receptors with ultralong CDR3s in dairy cattle have been limited by the number of animals examined (1-4 animals in each study), and by varying breeds and ages. The objective of this study was to assess the percentage of IgM and IgG sequences with ultralong CDR3s, and gene usage in blood and colostral lymphocytes from cows classified as high, average, and low immune responders based on their estimated breeding values. B lymphocytes were isolated from the blood of 14 heifers and 7 cows. In addition, cells were isolated from colostrum of the 7 cows. RNA was extracted, cDNA was produced, and IgM and IgG transcripts were amplified using polymerase chain reactions. Amplicons were sequenced using Oxford Nanopore long-read sequencing. In sequences derived from blood B cells, AMIR estimated breeding values were significantly and positively associated with higher percentages of IgG ultralong CDR3 sequences. High AMIR cows (n = 3) also produced colostrum with a significantly greater percentage of IgG ultralong CDR3 sequences (18.0 %) than average AMIR cows (n = 4, mean 8.8 %). Larger studies are needed to investigate the association between percentages of B cells expressing IgG ultralong CDR3s and observed health traits.

Genome-Wide Scans for Selection Signatures in Ningxia Angus Cattle Reveal Genetic Variants Associated with Economic and Adaptive Traits

The genetic improvement of beef cattle breeds is crucial for the advancement of the beef cattle industry. Whole-genome resequencing technology has been widely applied in genetic breeding as well as research on selection signatures in beef cattle. In this study, 20× whole-genome resequencing was performed on 282 Angus cattle from the Ningxia region, and a high-quality dataset encompassing extensive genomic variations across the entire genome was constructed. The iHS test identified 495 selection signal regions, which included pregnancy-associated glycoprotein (PAG) family genes and immune-related genes such as UL16-binding protein 21 (ULBP21), CD1b molecule (CD1B), and tumor necrosis factor ligand superfamily member 11 (TNFSF11). A quantitative trait locus (QTL) enrichment analysis revealed that several economic traits, including longissimus muscle area, marbling score, carcass weight, average daily gain, and milk yield, were significantly enriched in cattle with these selection signatures. Although the enrichment of QTLs for health traits was low, immune-related genes may indirectly contribute to improvements in production performance. These findings show the genetic basis of economic and adaptive traits in Ningxia Angus cattle, providing a theoretical foundation and guidance for further genetic improvement and breeding strategies.

Omonijo F, A Ganai N, M. Ibeagha-Awemu E, Mudasir Ahmad S. Immunotherapy in mastitis: state of knowledge, research gaps and way forward

Mastitis is an inflammatory condition that affects dairy cow's mammary glands. Traditional treatment approaches with antibiotics are increasingly leading to challenging scenarios such as antimicrobial resistance. In order to mitigate the unwanted side effects of antibiotics, alternative strategies such as those that harness the host immune system response, also known as immunotherapy, have been implemented. Immunotherapy approaches to treat bovine mastitis aims to enhance the cow's immune response against pathogens by promoting pathogen clearance, and facilitating tissue repair. Various studies have demonstrated the potential of immunotherapy for reducing the incidence, duration and severity of mastitis. Nevertheless, majority of reported therapies are lacking in specificity hampering their broad application to treat mastitis. Meanwhile, advancements in mastitis immunotherapy hold great promise for the dairy industry, with potential to provide effective and sustainable alternatives to traditional antibiotic-based approaches. This review synthesizes immunotherapy strategies, their current understanding and potential future perspectives. The future perspectives should focus on the development of precision immunotherapies tailored to address individual pathogens/group of pathogens, development of combination therapies to address antimicrobial resistance, and the integration of nano- and omics technologies. By addressing research gaps, the field of mastitis immunotherapy can make significant strides in the control, treatment and prevention of mastitis, ultimately benefiting both animal and human health/welfare, and environment health.

Breed variability in the cellular mediated immune response to experimental Neospora caninum infection in heifers

Protozoan parasite Neospora caninum causes abortion in infected cattle while others remain asymptomatic. Host immunity plays a critical role in the outcome of bovine neosporosis. Despite extensive research, there is a critical gap in therapeutic and preventive measures, and no effective vaccines are available. Both beef and dairy cattle can suffer from N. caninum-induced abortions, but cumulative evidence suggests a breed susceptibility being higher in dairy compared with beef breeds. It has been established that the response to N. caninum infection primarily involves a cell-mediated immune response (CMIR) regulated by T-helper type 1 (Th1) cells and specific cytokines. The delayed-type hypersensitivity (DTH) skin test has been used to measure the ability of livestock to generate CMIR, in the context of breeding for disease resistance and as a method for diagnosis of several diseases. In this study, we evaluated the immune response triggered by an N. caninum-induced DTH skin test between Holstein - a dairy breed intensively selected- and Argentinean Creole heifers - a beef breed with minimal genetic selection- to assess differences in CMIR following experimental N. caninum infection. The immune response, measured through skinfold thickness and histological and immune molecular analysis, revealed variations between the breeds. Our study found an increased CMIR in Argentinean Creole heifers compared to Holstein heifers. Differential gene expression of key cytokines was observed at the DTH skin test site. Argentinean Creole heifers exhibited elevated IFN-γ, IL-12, IL-10, and IL-4, while Holstein heifers only showed higher expression of IL-17. This finding could underscore genetic diversity in response to neosporosis, which could be used in breeding cattle strategies for disease resistance in cattle populations.

Survey on resistance occurrence for F4+ and F18+ enterotoxigenic Escherichia coli (ETEC) among pigs reared in Central Italy regions

Porcine Post Weaning Diarrhoea (PWD) is one of the most important swine disease worldwide, caused by Enterotoxigenic Escherichia coli (ETEC) strains able to provoke management, welfare and sanitary issues. ETEC is determined by proteinaceous surface appendages. Numerous studies conducted by now in pigs have demonstrated, at the enterocytes level, that, the genes mucin 4 (MUC4) and fucosyltransferase (FUT1), coding for ETEC F4 and F18 receptors respectively, can be carriers of single nucleotide polymorphisms (SNPs) associated with natural resistance/susceptibility to PWD. The latter aspect was investigated in this study, evaluating the SNPs of the MUC4 and FUT1 genes in slaughtered pigs reared for the most in Central Italy. Genomic DNA was extracted from 362 swine diaphragmatic samples and then was subjected to the detection of known polymorphisms on MUC4 and FUT1candidate target genes by PCR-RFLP. Some of the identified SNPs were confirmed by sequencing analysis. Animals carrying the SNPs associated with resistance were 11% and 86% for the FUT1 and MUC4 genes respectively. Therefore, it can be assumed that the investigated animals may be an important resource and reservoir of favorable genetic traits for the breeding of pigs resistant to enterotoxigenic E.coli F4 variant.

Impact of heat stress on dairy cattle and selection strategies for thermotolerance: a review

Climate change is a problem that causes many environmental issues that impact the productivity of livestock species. One of the major issues associated with climate change is an increase of the frequency of hot days and heat waves, which increases the risk of heat stress for livestock species. Dairy cattle have been identified as being susceptible to heat stress due to their high metabolic heat load. Studies have shown heat stress impacts several biological processes that can result in large economic consequences. When heat stress occurs, dairy cattle employ several physiological and cellular mechanisms in order to dissipate heat and protect cells from damage. These mechanisms require an increase and diversion in energy toward protection and away from other biological processes. Therefore, in turn heat stress in dairy cattle can lead numerous issues including reductions in milk production and reproduction as well as increased risk for disease and mortality. This indicates a need to select dairy cattle that would be thermotolerant. Various selection strategies to confer thermotolerance have been discussed in the literature, including selecting for reduced milk production, crossbreeding with thermotolerant breeds, selecting based on physiological traits and most recently selecting for enhanced immune response. This review discusses the various issues associated with heat stress in dairy cattle and the pros and cons to the various selection strategies that have been proposed to select for thermotolerance in dairy cattle.

Global genomic methylation related to the degree of parasitism in cattle

The objective of the present study was to characterize a herd of 72 ½ Angus × ½ Nellore heifers, identify the resistant, resilient and susceptible animals to parasites, relate the overall DNA methylation of these animals with the degree of parasitism, evaluated by the egg count per gram of feces (EPG), Haematobia irritans count (horn fly) and Rhipicephalus microplus count (bovine tick). The experiment was carried out in a completely randomized design, containing 72 treatments, with each animal considered a treatment, and 11 repetitions, with each collection within a year considered a repetition. The data obtained from the counts of the evaluated parasites were subjected to statistical analysis using the SISVAR program, to classify heifers according to the degree of parasitism in low (resistant), intermediary (resilient) and high (susceptible) parasite load for infection by nematodes, infestation by ticks and flies. Addition the animals in these three groups, by hierarchical grouping using the GENES program, heifers were classified as to the degree of parasitism by the three parasites along with the DNA methylation content of the animals in each group. A negative relationship was observed between resistance and methylated DNA content in both classifications, with the resistant, resilient, and susceptible animals showing the highest, intermediate, and lowest methylated DNA quantifications, respectively. Thus, the methodologies used herein enabled the classification of 72 heifers according to the degree of collective infection by gastrointestinal nematodes and infestation by ticks and horn flies, thereby establishing a link between the degree of parasitic resistance in cattle and the global methylated DNA quantification.

Cluster of Differentiation 24 Polymorphism Has No Significant Association with Chronic Hepatitis B Virus Infection in the Chinese Han Population: A Family-Based Association Study

OBJECTIVE

Studies have shown that cluster of differentiation (CD) 24 gene polymorphism is associated with several diseases. Among these, chronic hepatitis B (CHB) infection has not been investigated. This study aimed to assess the function of CD24 in CHB.

METHODS

The study included 478 cases of CHB and 318 cases without CHB from 230 families that underwent genotyping. Polymerase chain reaction-restriction fragment length polymorphism was performed to assess the single nucleotide polymorphism (SNP) P170 of the CD24 gene. The detected genotypes were TT, CT, and CC. Then, family based-association analysis was carried out to investigate the association between CD24 gene polymorphism and susceptibility to CHB.

RESULTS

In the 478 patients with CHB, the frequencies of CD24 P170 T and C alleles were 35.5% and 64.5%, respectively, and the frequencies of CD24 P170 CC, CT, and TT genotypes were 39.3%, 50.4% and 10.3%, respectively. In a CD24 single-locus analysis by a family-based association test of P170 polymorphisms, T and C were not significantly associated with CHB in the additive (Z = 0.169, P = 0.866; Z = -0.169, P = 0.866, respectively), dominant (Z = 0.522, P = 0.602; Z = 0.428, P = 0.669, respectively), or recessive (Z = -0.428, P = 0.669; Z = -0.522, P = 0.602, respectively) models. Transmission-disequilibrium (TD) and sib-transmission disequilibrium (STD) tests revealed no excess of T or C alleles from heterozygous parents to their children with the disease or higher frequencies of these alleles in patients compared with their normal siblings (χ 2 = 0.06, P = 0.897).

CONCLUSION

The study findings suggest that the SNP P170 of CD24 has no significant association with susceptibility to the HB virus and related phenotypes in Chinese patients.

Immuno-phenotyping of Canadian Beef Cattle: Adaptation of the High Immune Response Methodology for Utilization in Beef Cattle

The high immune response (HIR) methodology measures the genetic performance of the adaptive immune system to identify and breed animals with balanced and robust immunity. The HIR methodology has previously been used in dairy and swine to reduce disease but has not been fully investigated in beef cattle. The first objective of the current study was to examine whether the HIR methodology as standardized for use in dairy cattle was appropriate for use in beef cattle. The second objective was to determine the earliest age for immune response phenotyping of beef calves. In this study, beef calves (n = 295) of various ages, as well as mature beef cows (n = 170) of mixed breeds, were immunized using test antigens to assess their antibody- (AMIR) and cell-mediated immune responses (CMIR). Heritability for AMIR and CMIR was estimated at 0.43 and 0.18, respectively. The HIR methodology was appropriate for use in beef cattle; beef calves as young as 2–3 wk of age were capable of mounting AMIR responses comparable with those seen historically in mature Holstein dairy cows. Three-week-old beef calves mounted CMIR responses comparable with those of Holstein cows, but 9-mo-old calves and mature beef cows had significantly higher CMIR responses than Holsteins. The HIR methodology can be used to measure both AMIR and CMIR in beef calves as young as 3 wk of age.

Assessing the Outbreak Risk of Epidemics Using Fuzzy Evidential Reasoning

Epidemic diseases (EDs) present a significant but challenging risk endangering public health, evidenced by the outbreak of COVID-19. Compared to other risks affecting public health such as flooding, EDs attract little attention in terms of risk assessment in the current literature. It does not well respond to the high practical demand for advanced techniques capable of tackling ED risks. To bridge this gap, an adapted fuzzy evidence reasoning method is proposed to realize the quantitative analysis of ED outbreak risk assessment (EDRA) with high uncertainty in risk data. The novelty of this article lies in (1) taking the lead to establish the outbreak risk evaluation system of epidemics covering the whole epidemic developing process, (2) combining quantitative and qualitative analysis in the fields of epidemic risk evaluation, (3) collecting substantial first-hand data by reviewing transaction data and interviewing the frontier experts and policymakers from Chinese Centers for Disease Control and Chinese National Medical Products Administration. This work provides useful insights for the regulatory bodies to (1) understand the risk levels of different EDs in a quantitative manner and (2) the sensitivity of different EDs to the identified risk factors for their effective control. For instance, in the case study, we use real data to disclose that influenza has the highest breakout risk level in Beijing. The proposed method also provides a potential tool for evaluating the outbreak risk of COVID-19.

Impacts of Epigenetic Processes on the Health and Productivity of Livestock

The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.

The Autumn Low Milk Yield Syndrome in High Genetic Merit Dairy Cattle: The Possible Role of a Dysregulated Innate Immune Response

Simple Summary

Milk yield worldwide is dominated by few cosmopolitan dairy cattle breeds producing high production levels in the framework of hygiene standards that have dramatically improved over the years. Yet, there is evidence that such achievements have gone along with substantial animal health and welfare problems for many years, exemplified by reduced life expectancy and high herd replacement rates. Also, these animals are very susceptible to diverse environmental stressors, among which hot summer climate plays a central role in the occurrence of diverse disease cases underlying early cull from the herd. Milk production is also affected by heat stress, both directly and indirectly, as shown by low milk yield in the following autumn period. This article highlights the low milk yield syndrome and sets it into a conceptual framework, based on the crucial role of the innate immune system in the response to non-infectious stressors and in adaptation physiology at large.

Abstract

The analysis of milk yield data shows that high genetic merit dairy cows do not express their full production potential in autumn. Therefore, we focused on metabolic stress and inflammatory response in the dry and peripartum periods as possible causes thereof. It was our understanding that some cows could not cope with the stress imposed by their physiological and productive status by means of adequate adaptation strategies. Accordingly, this study highlights the noxious factors with a potential to affect cows in the above transition period: hot summer climate, adverse genetic traits, poor coping with unfavorable environmental conditions, outright production diseases and consequences thereof. In particular, the detrimental effects in the dry period of overcrowding, photoperiod change and heat stress on mammary gland development and milk production are highlighted in the context of the autumn low milk yield syndrome. The latter could be largely accounted for by a “memory” effect on the innate immune system induced in summer by diverse stressors after dry-off, according to strong circumstantial and indirect experimental evidence. The “memory” effect is based on distinct epigenetic changes of innate immunity genes, as already shown in cases of bovine mastitis. Following a primary stimulation, the innate immune system would be able to achieve a state known as “trained immunity”, a sort of “education” which modifies the response to the same or similar stressors upon a subsequent exposure. In our scenario, the “education” of the innate immune system would induce a major shift in the metabolism of inflammatory cells following their reprogramming. This would entail a higher basal consumption of glucose, in competition with the need for the synthesis of milk. Also, there is strong evidence that the inflammatory response generated in the dry period leads to a notable reduction of dry matter intake after calving, and to a reduced efficiency of oxidative phosphorylation in mitochondria. On the whole, an effective control of the stressors in the dry period is badly needed for better disease control and optimal production levels in dairy cattle.

Why breed disease-resilient livestock, and how?

BACKGROUND

Fighting and controlling epidemic and endemic diseases represents a considerable cost to livestock production. Much research is dedicated to breeding disease resilient livestock, but this is not yet a common objective in practical breeding programs. In this paper, we investigate how future breeding programs may benefit from recent research on disease resilience.

MAIN BODY

We define disease resilience in terms of its component traits resistance (R: the ability of a host animal to limit within-host pathogen load (PL)) and tolerance (T: the ability of an infected host to limit the damage caused by a given PL), and model the host's production performance as a reaction norm on PL, depending on R and T. Based on this, we derive equations for the economic values of resilience and its component traits. A case study on porcine respiratory and reproductive syndrome (PRRS) in pigs illustrates that the economic value of increasing production in infectious conditions through selection for R and T can be more than three times higher than by selection for production in disease-free conditions. Although this reaction norm model of resilience is helpful for quantifying its relationship to its component traits, its parameters are difficult and expensive to quantify. We consider the consequences of ignoring R and T in breeding programs that measure resilience as production in infectious conditions with unknown PL-particularly, the risk that the genetic correlation between R and T is unfavourable (antagonistic) and that a trade-off between them neutralizes the resilience improvement. We describe four approaches to avoid such antagonisms: (1) by producing sufficient PL records to estimate this correlation and check for antagonisms-if found, continue routine PL recording, and if not found, shift to cheaper proxies for PL; (2) by selection on quantitative trait loci (QTL) known to influence both R and T in favourable ways; (3) by rapidly modifying towards near-complete resistance or tolerance, (4) by re-defining resilience as the animal's capacity to resist (or recover from) the perturbation caused by an infection, measured as temporal deviations of production traits in within-host longitudinal data series.

CONCLUSIONS

All four alternatives offer promising options for genetic improvement of disease resilience, and most rely on technological and methodological developments and innovation in automated data generation.

Transcriptomic Profiles of Monocyte-Derived Macrophages in Response to Escherichia coli is Associated with the Host Genetics

Reactive Nitrogen Species (RNS) are a group of bactericidal molecules produced by macrophages in response to pathogens in a process called oxidative burst. Nitric oxide (NO^-) is a member of RNS produced from arginine by inducible Nitric Oxide Synthase (iNOS) enzyme. The activity of iNOS and production of NO^- by macrophages following stimulation is one of the indicators of macrophage polarization towards M1/proinflammatory. Production of NO^- by bovine monocyte-derived macrophage (MDM) and mouse peritoneal macrophages has been shown to be strongly associated with host genetic with the heritability of 0.776 in bovine MDM and 0.8 in mouse peritoneal macrophages. However, the mechanism of genetic regulation of macrophage response has remained less explored. In the current study, the transcriptome of bovine MDMs was compared between two extreme phenotypes that had been classified as high and low responder based on NO^- production. The results showed that 179 and 392 genes were differentially expressed (DE) between high and low responder groups at 3 and 18 hours after exposure to Escherichia coli, respectively. A set of 11 Transcription Factors (TFs) (STAT1, IRF7, SPI1, STAT4, IRF1, HIF1A, FOXO3, REL, NFAT5, HIC1, and IRF4) at 3 hours and a set of 13 TFs (STAT1, IRF1, HIF1A, STAT4, ATF4, TP63, EGR1, CDKN2A, RBL1, E2F1, PRDM1, GATA3, and IRF4) at 18 hours after exposure to E. coli were identified to be differentially regulated between the high and low responder phenotypes. These TFs were found to be divided into two clusters of inflammatory- and hypoxia-related TFs. Functional analysis revealed that some key canonical pathways such as phagocytosis, chemotaxis, antigen presentation, and cell-to-cell signalling are enriched among the over-expressed genes by high responder phenotype. Based on the results of this study, it was inferred that the functional characteristics of bovine MDMs are associated with NO-based classification. Since NO^- production is strongly associated with host genetics, this study for the first time shows the distinct proinflammatory profiles of macrophages are controlled by the natural genetic polymorphism in an outbred population. In addition, the results suggest that genetics can be considered as a new dimension in the current model of macrophage polarization which is currently described by the combination of stimulants, only.