DNA variation in the gene ELTD1 is associated with tick burden in cattle

Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis

Background

Disease emergence and production loss caused by cattle tick infestations have focused attention on genetic selection strategies to breed beef cattle with increased tick resistance. However, the mechanisms behind host responses to tick infestation have not been fully characterised. Hence, this study examined gene expression profiles of peripheral blood leukocytes from tick-naive Brangus steers (Bos taurus x Bos indicus) at 0, 3, and 12 weeks following artificial tick challenge experiments with Rhipicephalus australis larvae. The aim of the study was to investigate the effect of tick infestation on host leukocyte response to explore genes associated with the expression of high and low host resistance to ticks.

Results

Animals with high (HR, n = 5) and low (LR, n = 5) host resistance were identified after repeated tick challenge. A total of 3644 unique differentially expressed genes (FDR < 0.05) were identified in the comparison of tick-exposed (both HR and LR) and tick-naive steers for the 3-week and 12-week infestation period. Enrichment analyses showed genes were involved in leukocyte chemotaxis, coagulation, and inflammatory response. The IL-17 signalling, and cytokine-cytokine interactions pathways appeared to be relevant in protection and immunopathology to tick challenge. Comparison of HR and LR phenotypes at timepoints of weeks 0, 3, and 12 showed there were 69, 8, and 4 differentially expressed genes, respectively. Most of these genes were related to immune, tissue remodelling, and angiogenesis functions, suggesting this is relevant in the development of resistance or susceptibility to tick challenge.

Conclusions

This study showed the effect of tick infestation on Brangus cattle with variable phenotypes of host resistance to R. australis ticks. Steers responded to infestation by expressing leukocyte genes related to chemotaxis, cytokine secretion, and inflammatory response. The altered expression of genes from the bovine MHC complex in highly resistant animals at pre- and post- infestation stages also supports the relevance of this genomic region for disease resilience. Overall, this study offers a resource of leukocyte gene expression data on matched tick-naive and tick-infested steers relevant for the improvement of tick resistance in composite cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08686-3.

ELTD1-An Emerging Silent Actor in Cancer Drama Play

The epidermal growth factor, latrophilin, and seven transmembrane domain–containing protein 1 (ELTD1), is a member of the G–protein coupled receptors (GPCRs) superfamily. Although discovered in 2001, ELTD1 has been investigated only by a few research groups, and important data about its role in normal and tumor cells is still missing. Even though its functions and structure are not yet fully understood, recent studies show that ELTD1 has a role in both physiological and pathological angiogenesis, and it appears to be a very important biomarker and a molecular target in cancer diseases. Upregulation of ELTD1 in malignant cells has been reported, and correlated with poor cancer prognosis. This review article aims to compile the existing data and to discuss the current knowledge on ELTD1 structure and signaling, and its role in physiological and neoplastic conditions.

Signatures of Selection in Composite Vrindavani Cattle of India

Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle. The constituent breeds were selected for higher milk production and adaptation to the tropical climate. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. A total of 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). The Vrindavani breed was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (F_ST). We identified 11 common regions detected by more than one method harboring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B, and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.

ELTD1 facilitates glioma proliferation, migration and invasion by activating JAK/STAT3/HIF-1α signaling axis

The upregulation of ELTD1 ([epidermal growth factor (EGF), latrophilin and seven transmembrane domain-containing 1] on chromosome 1) in tumor cells has been reported in several types of cancer and correlates with poor cancer prognosis. However, the role of ELTD1 in glioma progression remains unknown. In this study, we examined ELTD1 expression levels in human glioma cell lines and in sixteen human gliomas of different grades. The molecular effects of ELTD1 in glioma cells were measured using quantitative polymerase chain reaction (qRT-PCR), Western blotting, Cell proliferation assays, Matrigel migration and invasion assays and brain orthotopic xenografts. We found that high expression levels of ELTD1 were positively associated with cancer progression and poor prognosis in human glioma. Mechanistically, ELTD1 activated the JAK/STAT3/HIF-1α signaling axis and p-STAT3 bound with HIF-1α. Taken together, our data provide a plausible mechanism for ELTD1-modulated glioma progression and suggest that ELTD1 may represent a potential therapeutic target in the prevention and therapy of glioma.

Genomic clues of the evolutionary history of Bos indicus cattle

Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.

Towards a new phenotype for tick resistance in beef and dairy cattle: a review

About 80% of the world’s cattle are affected by ticks and tick-borne diseases, both of which cause significant production losses. Cattle host resistance to ticks is the most important factor affecting the economics of tick control, but it is largely neglected in tick-control programs due to technical difficulties and costs associated with identifying individual-animal variation in resistance. The present paper reviews the scientific literature to identify factors affecting resistance of cattle to ticks and the biological mechanisms of host tick resistance, to develop alternative phenotype(s) for tick resistance. If new cost-effective phenotype(s) can be developed and validated, then tick resistance of cattle could be genetically improved using genomic selection, and incorporated into breeding objectives to simultaneously improve cattle productive attributes and tick resistance. The phenotype(s) could also be used to improve tick control by using cattle management. On the basis of the present review, it is recommended that three possible phenotypes (haemolytic analysis; measures of skin hypersensitivity reactions; simplified artificial tick infestations) be further developed to determine their practical feasibility for consistently, cost-effectively and reliably measuring cattle tick resistance in thousands of individual animals in commercial and smallholder farmer herds in tropical and subtropical areas globally. During evaluation of these potential new phenotypes, additional measurements should be included to determine the possibility of developing a volatile-based resistance phenotype, to simultaneously improve cattle resistance to both ticks and biting flies. Because the current measurements of volatile chemistry do not satisfy the requirements of a simple, cost-effective phenotype for use in commercial cattle herds, consideration should also be given to inclusion of potentially simpler measures to enable indirect genetic selection for volatile-based resistance to ticks.

Cattle Tick Rhipicephalus microplus-Host Interface: A Review of Resistant and Susceptible Host Responses

Ticks are able to transmit tick-borne infectious agents to vertebrate hosts which cause major constraints to public and livestock health. The costs associated with mortality, relapse, treatments, and decreased production yields are economically significant. Ticks adapted to a hematophagous existence after the vertebrate hemostatic system evolved into a multi-layered defense system against foreign invasion (pathogens and ectoparasites), blood loss, and immune responses. Subsequently, ticks evolved by developing an ability to suppress the vertebrate host immune system with a devastating impact particularly for exotic and crossbred cattle. Host genetics defines the immune responsiveness against ticks and tick-borne pathogens. To gain an insight into the naturally acquired resistant and susceptible cattle breed against ticks, studies have been conducted comparing the incidence of tick infestation on bovine hosts from divergent genetic backgrounds. It is well-documented that purebred and crossbred Bos taurus indicus cattle are more resistant to ticks and tick-borne pathogens compared to purebred European Bos taurus taurus cattle. Genetic studies identifying Quantitative Trait Loci markers using microsatellites and SNPs have been inconsistent with very low percentages relating phenotypic variation with tick infestation. Several skin gene expression and immunological studies have been undertaken using different breeds, different samples (peripheral blood, skin with tick feeding), infestation protocols and geographic environments. Susceptible breeds were commonly found to be associated with the increased expression of toll like receptors, MHC Class II, calcium binding proteins, and complement factors with an increased presence of neutrophils in the skin following tick feeding. Resistant breeds had higher levels of T cells present in the skin prior to tick infestation and thus seem to respond to ticks more efficiently. The skin of resistant breeds also contained higher numbers of eosinophils, mast cells and basophils with up-regulated proteases, cathepsins, keratins, collagens and extracellular matrix proteins in response to feeding ticks. Here we review immunological and molecular determinants that explore the cattle tick Rhipicephalus microplus-host resistance phenomenon as well as contemplating new insights and future directions to study tick resistance and susceptibility, in order to facilitate interventions for tick control.

Analyses of reaction norms reveal new chromosome regions associated with tick resistance in cattle

Despite single nucleotide polymorphism (SNP) availability and frequent cost reduction has allowed genome-wide association studies even in complex traits as tick resistance, the use of this information source in SNP by environment interaction context is unknown for many economically important traits in cattle. We aimed at identifying putative genomic regions explaining differences in tick resistance in Hereford and Braford cattle under SNP by environment point of view as well as to identify candidate genes derived from outliers/significant markers. The environment was defined as contemporary group means of tick counts, since they seemed to be the most appropriate entities to describe the environmental gradient in beef cattle. A total of 4363 animals having tick counts (n=10 673) originated from 197 sires and 3966 dams were used. Genotypes were acquired on 3591 of these cattle. From top 1% SNPs (410) having the greatest effects in each environment, 75 were consistently relevant in all environments, which indicated SNP by environment interaction. The outliers/significant SNPs were mapped on chromosomes 1, 2, 5, 6, 7, 9, 11, 13, 14, 15, 16, 18, 21, 23, 24, 26 and 28, and potential candidate genes were detected across environments. The presence of SNP by environment interaction for tick resistance indicates that genetic expression of resistance depends upon tick burden. Markers with major portion of genetic variance explained across environments appeared to be close to genes with different direct or indirect functions related to immune system, inflammatory process and mechanisms of tissue destruction/repair, such as energy metabolism and cell differentiation.

Tag SNP selection for prediction of tick resistance in Brazilian Braford and Hereford cattle breeds using Bayesian methods

BACKGROUND

Cattle resistance to ticks is known to be under genetic control with a complex biological mechanism within and among breeds. Our aim was to identify genomic segments and tag single nucleotide polymorphisms (SNPs) associated with tick-resistance in Hereford and Braford cattle. The predictive performance of a very low-density tag SNP panel was estimated and compared with results obtained with a 50 K SNP dataset.

RESULTS

BayesB (π = 0.99) was initially applied in a genome-wide association study (GWAS) for this complex trait by using deregressed estimated breeding values for tick counts and 41,045 SNP genotypes from 3455 animals raised in southern Brazil. To estimate the combined effect of a genomic region that is potentially associated with quantitative trait loci (QTL), 2519 non-overlapping 1-Mb windows that varied in SNP number were defined, with the top 48 windows including 914 SNPs and explaining more than 20% of the estimated genetic variance for tick resistance. Subsequently, the most informative SNPs were selected based on Bayesian parameters (model frequency and t-like statistics), linkage disequilibrium and minor allele frequency to propose a very low-density 58-SNP panel. Some of these tag SNPs mapped close to or within genes and pseudogenes that are functionally related to tick resistance. Prediction ability of this SNP panel was investigated by cross-validation using K-means and random clustering and a BayesA model to predict direct genomic values. Accuracies from these cross-validations were 0.27 ± 0.09 and 0.30 ± 0.09 for the K-means and random clustering groups, respectively, compared to respective values of 0.37 ± 0.08 and 0.43 ± 0.08 when using all 41,045 SNPs and BayesB with π = 0.99, or of 0.28 ± 0.07 and 0.40 ± 0.08 with π = 0.999.

CONCLUSIONS

Bayesian GWAS model parameters can be used to select tag SNPs for a very low-density panel, which will include SNPs that are potentially linked to functional genes. It can be useful for cost-effective genomic selection tools, when one or a few key complex traits are of interest.

Epidermal growth factor, latrophilin, and seven transmembrane domain-containing protein 1 marker, a novel angiogenesis marker

Epidermal growth factor, latrophilin, and seven transmembrane domain-containing protein 1 on chromosome 1 (ELTD1), an orphan adhesion G-protein coupled receptor, was reported as a regulator of angiogenesis, also involved in cancer progression and development. More recently, ELTD1 was identified as a potential new tumor marker for high-grade glioma. ELTD1, belongs to the G-protein coupled receptor superfamily that comprises the biggest receptor family in the human genome. Following the discovery of ELTD1 almost a decade ago, only a few research groups have attempted to find its role in normal and tumor cells, important information about this receptor remaining still unknown. The ELTD1 ligand has not currently been identified and intracellular signaling studies have not yet been performed in normal or tumor cells. Although the current published data on ELTD1 function and structure are rather limited, this receptor seems to be very important, not only as biomarker, but also as molecular target in glioblastoma. This review summarizes and discusses the current knowledge on ELTD1 structure, function, and its role in both physiological and tumoral angiogenesis.

A review of ELTD1, a pro-angiogenic adhesion GPCR

Epidermal growth factor, latrophilin and seven-transmembrane domain-containing 1 (ELTD1), an orphan G-protein-coupled receptor (GPCR) belonging to the adhesion GPCR family, has recently been identified as a potential cancer biomarker and a novel regulator of angiogenesis. In this mini-review, we present an overview of the current literature on ELTD1 and present bioinformatics data showing ELTD1's sequence conservation, its expression in cancer cell lines and its mutational frequency in human cancers. Additionally, we present sequence homology alignment results confirming ELTD1 to be a hybrid comprising motifs shared with individual members in both adhesion GPCR subfamilies 1 and 2. Finally, we discuss why tumour endothelial ELTD1 expression may confer a good prognosis yet still represent a therapeutic target.

ELTD1, a potential new biomarker for gliomas

BACKGROUND

Glioblastoma multiforme (GBM), a high-grade glioma, is characterized by being diffuse, invasive, and highly angiogenic and has a very poor prognosis. Identification of new biomarkers could help in the further diagnosis of GBM.

OBJECTIVE

To identify ELTD1 (epidermal growth factor, latrophilin, and 7 transmembrane domain-containing protein 1 on chromosome 1) as a putative glioma-associated marker via a bioinformatic method.

METHODS

We used advanced data mining and a novel bioinformatics method to predict ELTD1 as a potential novel biomarker that is associated with gliomas. Validation was done with immunohistochemistry, which was used to detect levels of ELTD1 in human high-grade gliomas and rat F98 glioma tumors. In vivo levels of ELTD1 in rat F98 gliomas were assessed using molecular magnetic resonance imaging.

RESULTS

ELTD1 was found to be significantly higher (P = .03) in high-grade gliomas (50 patients) compared with low-grade gliomas (21 patients) and compared well with traditional immunohistochemistry markers including vascular endothelial growth factor, glucose transporter 1, carbonic anhydrase IX, and hypoxia-inducible factor 1α. ELTD1 gene expression indicates an association with grade, survival across grade, and an increase in the mesenchymal subtype. Significantly high (P < .001) in vivo levels of ELTD1 were additionally found in F98 tumors compared with normal brain tissue.

CONCLUSION

Results of this study strongly suggests that associative analysis was able to accurately identify ELTD1 as a putative glioma-associated biomarker. The detection of ELTD1 was also validated in both rodent and human gliomas and may serve as an additional biomarker for gliomas in preclinical and clinical diagnosis of gliomas.

Breeding strategies for tick resistance in tropical cattle: a sustainable approach for tick control

About 80 % of world cattle population is under the risk of ticks and tick borne diseases (TTBDs). Losses caused by bovine tick burdens in tropical countries have a tremendous economic impact on production systems. Chemical control of disease has been found to be ineffective and also involving large cost. To reduce our reliance on these chemical products, it is necessary to embark on programs that include habitat management, genetic selection of hosts, and development of a strain capable of inducing host resistance to ticks. Selection for disease resistance provide alternate method for sustainable control of TTBDs. Domestic livestock manifests tick-resistance by skin thickness, coat type, coat color, hair density and skin secretions etc. Zebu cattle have, on average, greater tick resistance than either European cattle or African cattle. Heritability for tick burden in cattle has been shown to range about 0.30, which is sufficient to result in the success of some programs of selection for tick resistance in cattle. To select animals at younger age, to reduce generation interval and to increase genetic gain, marker assisted selection is an important tool. There are also various MHC molecules which are associated with resistance to TTBDs.

The brominated compound aeroplysinin-1 inhibits proliferation and the expression of key pro- inflammatory molecules in human endothelial and monocyte cells

Aeroplysinin-1 is a brominated antibiotic used by some sponges for defense against bacterial pathogen invasion. Aeroplysinin-1 has a wide spectrum of anti-tumoral action and behaves as a potent anti-angiogenic compound for bovine aortic endothelial cells. In this study, we demonstrate anti-angiogenic effects of aeroplysinin-1 on human endothelial cells. Furthermore, the response of angiogenesis related genes to aeroplysinin-1 treatment was studied in human endothelial cells by using gene arrays. The major changes were observed in thrombospondin 1 (TSP-1) and monocyte chemoattractant protein-1 (MCP-1), both of which were down-regulated. These inhibitory effects of aeroplysinin-1 were confirmed by using independent experimental approaches. To have a deeper insight on the anti-inflammatory effects of aeroplysinin-1 in endothelial cells, cytokine arrays were also used. This experimental approach confirmed effects on MCP-1 and TSP-1 and showed down-regulation of several other cytokines. Western blotting experiments confirmed down-regulation of ELTD1 (EGF, latrophilin and seven transmembrane domain-containing protein 1), interleukin 1α and matrix metalloproteinase 1 (MMP-1). These results along with our observation of a dramatic inhibitory effect of aeroplysinin-1 on cyclooxygenase-2 protein expression levels in endothelial cells and a human monocyte cell line suggest that aeroplysinin-1 could be a novel anti-inflammatory compound with potential pharmacological interest.

Diversity and linkage disequilibrium features in a composite public/private dent maize panel: consequences for association genetics as evaluated from a case study using flowering time

Recent progress in genotyping and resequencing techniques have opened new opportunities for deciphering quantitative trait variation by looking for associations between traits of interest and polymorphisms in panels of diverse inbred lines. Association mapping raises specific issues related to the choice of appropriate (i) panels and marker-densities and (ii) statistical methods to capture associations. In this study, we used a panel of 314 maize inbred lines from the dent pool, composed of inbred material from public institutes (113 inbred lines) and a private company (201 inbred lines). We showed that local LD was higher and genetic diversity lower in the material of private origin than in the public material. We compared the results obtained by different software for identifying population structure and computing relatedness among lines, and ran association tests for earliness related traits. Our results confirmed the importance of the mite polymorphism of Vgt1 on flowering time, but also showed that its effect can be captured by zmRap2.7 polymorphisms located 70 kb apart. We also highlighted associations with polymorphisms within genes putatively involved in lignin biosynthesis pathway, which deserve further investigations.

The RIPK2 gene: a positional candidate for tick burden supported by genetic associations in cattle and immunological response of knockout mouse

Ticks and tick-borne diseases have a detrimental impact on livestock production causing estimated losses of around $200 million per year in Australia alone. Host resistance to ticks is heritable, within-breed heritability estimates being around 0.35, and with large differences between breeds. Previously a QTL for tick burden was detected on BTA14 at ~72 Mb distal to the centromere, near the gene receptor-interacting serine-threonine kinase 2 (RIPK2). To identify polymorphisms in this region, we sequenced all exons of the RIPK2 gene, identifying 46 single nucleotide polymorphism (SNP). Using SNP from RIPK2 as well as SNP from the bovine genome sequence, we genotyped two samples, one of 1,122 taurine dairy cattle and one of 761 zebu and zebu composite beef cattle. We confirmed that SNP and haplotypes from this region, including from RIPK2, were associated with tick burden in both dairy and beef cattle. To determine whether RIPK2 influences response to tick salivary gland extract (SGE), an immunisation experiment with tick SGE in a RIPK2 knockout (RIPK2 −/−) mouse strain was conducted. There was a significant (P < 0.05) reduction in IgG production in the RIPK2 −/− mouse in response to the SGE compared to its background strain C57BL/ 6 as well as the outbred CD1 mouse strain. In addition, antibodies generated by RIPK2 −/− mice recognised a different set of antigens within SGE when compared to parental-derived antibodies. In summary, the SNP association with tick burden at BTA14 was confirmed and quantitative and qualitative differences in antibody production were observed between RIPK2 −/− and wild-type mice.

Molecular genetic approaches for identifying the basis of variation in resistance to tick infestation in cattle

In recent years there has been renewed interest in the adaptation of cattle to challenging environments, largely driven by advances in genomic methods. The current interest in tick resistance is understandable given the major production and welfare implications of tick infestation in tropical and subtropical zones where around 70% of beef cattle are located. Heritability for tick burden in cattle has been shown to range about 0.30, which is sufficient to result in the success of some programs of selection for tick resistance in cattle. Gene-expression studies strongly indicate that both immune and non-immune mechanisms are associated with tick resistance in cattle. Recent quantitative-trait mapping studies have identified chromosome segments and single nucleotide polymorphisms associated with tick burden, but no causal variant has been identified so far. Most of the genetic markers identified for tick burden explain a relatively small proportion of the variance, which is typical of markers for quantitative traits. This leads to the conclusion that panels of multiple markers for tick resistance rather than a single marker will most likely be developed, possibly involving specific panels for zebu or taurine breeds, which could be used for future selection and breeding programs in cattle.