Increased expression of a novel splice variant of the complement component 4 (C4A) gene in mastitis-infected dairy cattle

Alternative splicing of pre-mRNA modulates the immune response in Holstein cattle naturally infected with Mycobacterium avium subsp. paratuberculosis

Little is known about the role of alternative splicing (AS) in regulating gene expression in Mycobacteria-infected individuals in distinct stages of infection. Pre-mRNA AS consists of the removal of introns and the assembly of exons contained in eukaryotic genes. AS events can influence transcript stability or structure with important physiological consequences. Using RNA-Seq data from peripheral blood (PB) and ileocecal valve (ICV) samples collected from Holstein cattle with focal and diffuse paratuberculosis (PTB)-associated histopathological lesions in gut tissues and without lesions (controls), we detected differential AS profiles between the infected and control groups. Four of the identified AS events were experimentally validated by reverse transcription-digital droplet PCR (RT-ddPCR). AS events in several genes correlated with changes in gene expression. In the ICV of animals with diffuse lesions, for instance, alternatively spliced genes correlated with changes in the expression of genes involved in endocytosis, antigen processing and presentation, complement activation, and several inflammatory and autoimmune diseases in humans. Taken together, our results identified common mechanisms of AS involvement in the pathogenesis of PTB and human diseases and shed light on novel diagnostic and therapeutic interventions to control these diseases.

Genome-wide alternative splicing profile in the posterior kidney of brown trout (Salmo trutta) during proliferative kidney disease

BACKGROUND

The cnidarian myxozoan parasite Tetracapsuloides bryosalmonae causes chronic proliferative kidney disease (PKD) in salmonids. This parasite is a serious threat to wild and cultured salmonids. T. bryosalmonae undergoes intra-luminal sporogonic development in the kidney of brown trout (Salmo trutta) and the viable spores are released via urine. We investigated the alternative splicing pattern in the posterior kidney of brown trout during PKD.

RESULTS

RNA-seq data were generated from the posterior kidney of brown trout collected at 12 weeks post-exposure to T. bryosalmonae. Subsequently, this data was mapped to the brown trout genome. About 153 significant differently expressed alternatively spliced (DEAS) genes, (delta PSI = 5%, FDR P-value < 0.05) were identified from 19,722 alternatively spliced events. Among the DEAS genes, the least and most abundant alternative splicing types were alternative 5' splice site (5.23%) and exon skipping (70.59%), respectively. The DEAS genes were significantly enriched for sodium-potassium transporter activity and ion homeostasis (ahcyl1, atp1a3a, atp1a1a.1, and atp1a1a.5). The protein-protein interaction network analysis enriched two local network clusters namely cation transporting ATPase C-terminus and Sodium/potassium ATPase beta chain cluster, and mixed inclusion of Ion homeostasis and EF-hand domain cluster. Furthermore, the human disease-related salmonella infection pathway was significantly enriched in the protein-protein interaction network.

CONCLUSION

This study provides the first baseline information about alternative splicing in brown trout during PKD. The generated data lay a foundation for further functional molecular studies in PKD - brown trout infection model. The information generated from the present study can help to develop therapeutic strategies for PKD in the future.

Gene expression adjustment of inflammatory mechanisms in dairy cow mammary gland parenchyma during host defense against staphylococci

The aim of the study was to identify differences in the expression of splice variants of the PRMT2, LTF and C4A genes in the mammary glands of healthy dairy cows and those infected with staphylococci. An expression study was conducted on 38 Polish Holstein-Friesian dairy cows who were removed from the herd owing to subclinical and chronic mastitic or reproductive issues. Two days before slaughter, milk samples were taken for microbiological analysis and examined for the presence of bacteria. The mammary gland parenchyma samples with a predominance of secretory tissue were taken; these were divided into three groups according to the health status of the mammary gland: H (without pathogenic bacteria in milk), CoNS (with coagulase-negative staphylococci in milk), and CoPS (with coagulase-positive staphylococci in milk). Two of the investigated genes, LTF and C4A, demonstrated variants unequivocally expressed in infected tissue. Two LTF gene variants were found to be associated with cow health status, and with the type of bacteria causing mastitis (CoPS or CoNS). In addition, the expression of C4A isoforms differed with regard to mastitis etiology groups. The comprehensive evaluation of PRMT2 transcript suggested that the gene may also be involved in course of mastitis: two of four PRMT2 transcripts showed increased expression in the mammary gland of the CoPS group compared to controls. The obtained results are important for the knowledge on the etiology of bovine mastitis. The effects of the identified mastitis-relevant splice variants need to be further explored on the protein level to verify the suitability of splice variants and recognize their contribution towards the disease phenotypes and course.

Structural and functional analysis of the signaling lymphocytic activation molecule family 7 (SLAMF7) gene in response to infection with coagulase-negative and coagulase-positive staphylococci

Splice variants of the signaling lymphocytic activation molecule family 7 (SLAMF7) gene have been identified, and differences in the expression of this gene have been demonstrated at the mRNA level in the mammary glands of healthy and mastitis-infected dairy cows. At the same time, significant associations have been found between a deletion in the SLAM7 gene exon, the occurrence of different splice variants, and the occurrence of mastitis in one group of dairy cows. An expression study was conducted on 40 Polish Holstein-Friesian dairy cows of the Black and White variety (group I). Milk samples were taken for microbiological analysis 2 d before slaughter and examined for the presence of bacteria. Immediately after slaughter, mammary tissue samples were taken and divided into 3 groups according to the health status of the mammary gland: healthy (without pathogenic bacteria in milk), coagulase-negative staphylococci (CNS), and coagulase-positive staphylococci (CPS). Based on different SLAMF7 gene DNA fragments, 2 alternative variants of this gene (V1 and V2) and complete gene expression were identified. Separate analyses performed for each isoform showed that the health status of the cow was strongly associated with the expression level of individual variants. The highest expression was detected for the SLAMF7 complete amplicon in healthy cows, and in the CNS and CPS cows the expression of this variant was also higher than V1 and V2. Sanger sequencing was applied to detect the polymorphism/indel variant in the second exon of the SLAMF7 gene probably having the greatest effect on the protein structure and function of SLAMF7. Two genotypes were detected: AA (wild-type) and AB (insertion A). In healthy cows, the frequency of homozygotes AA was higher than the heterozygotes, whereas in the infected animals, the genotypic distribution was the opposite. An association analysis between the identified polymorphism and production traits-including somatic cell count, as well as lactose, protein, and casein content and yield as indicators of subclinical mastitis occurrence-was performed on the group II cows (166 Polish Holstein-Friesian dairy cows). Unfortunately, due to the low number of AB animals, no relationship was demonstrated between genotype in the second exon and the health status of cows. Additionally, the difference in the percentage of SLAMF7-targeted DNA methylation between the groups of animals was not significant, with an average of ∼66 to 68%.

Post-transcriptional regulation through alternative splicing after infection with Flavobacterium columnare in channel catfish (Ictalurus punctatus)

Columnaris disease has long been recognized as a serious problem worldwide which affects both wild and cultured freshwater fish including the commercially important channel catfish (Ictalurus punctatus). The fundamental molecular mechanisms of the host immune response to the causative agent Flavobacterium columnare remain unclear, though gene expression analysis after the bacterial infection has been conducted. Alternative splicing, a post-transcriptional regulation process to modulate gene expression and increase the proteomic diversity, has not yet been studied in channel catfish following infection with F. columnare. In this study, genomic information and RNA-Seq datasets of channel catfish were used to characterize the changes of alternative splicing after the infection. Alternative splicing was shown to be induced by F. columnare infection, with 8.0% increase in alternative splicing event at early infection stage. Intriguingly, genes involved in RNA binding and RNA splicing themselves were significantly enriched in differentially alternatively spliced (DAS) gene sets after infection. This finding was consistent with our previous study in channel catfish following infection with Edwardsiella ictaluri. It was suggested to be a universal mechanism that genes involved in RNA binding and splicing were regulated to undergo differential alternative splicing after stresses in channel catfish. Moreover, many immune genes were observed to be differentially alternatively spliced after infection. Further studies need to be performed to get a deeper view of molecular regulation on alternative splicing after stresses, setting a foundation for developing catfish broodstocks with enhanced disease resistance.

Transcriptomics and iTRAQ-Proteomics Analyses of Bovine Mammary Tissue with Streptococcus agalactiae-Induced Mastitis

Mastitis is a highly prevalent disease in dairy cows that causes large economic losses. Streptococcus agalactiae is a common contagious pathogen and a major cause of bovine mastitis. The immune response to intramammary infection with S. agalactiae in dairy cows is a very complex biological process. To understand the host immune response to S. agalactiae-induced mastitis, mammary gland of lactating Chinese Holstein cows was challenged with S. agalactiae via nipple tube perfusion. Visual inspection, analysis of milk somatic cell counts, histopathology, and transmission electron microscopy of mammary tissue were performed to confirm S. agalactiae-induced mastitis. Microarray and isobaric tags for relative and absolute quantitation (iTRAQ) were used to compare the transcriptomes and proteomes of healthy and mastitic mammary tissue. Compared with healthy tissue, a total of 129 differentially expressed genes (DEGs, fold change >2, p < 0.05) and 144 differentially expressed proteins (DEPs, fold change >1.2, p < 0.05) were identified in mammary tissue from S. agalactiae-challenged cows. Among the concordant 18 DEGs/DEPs, immunoglobulin M precursor, cathelicidin-7 precursor, integrin alpha-5, and complement C4-A-like isoform X1 were associated with mastitis. Intramammary infection with S. agalactiae triggered a complex host innate immune response that involved complement and coagulation cascades, ECM-receptor interaction, focal adhesion, and phagosome and bacterial invasion of epithelial cells pathways. These results provide candidate genes or proteins for further studies in the context of prevention and targeted treatment of bovine mastitis.

Effect of complement component 5 polymorphisms on mastitis resistance in Egyptian buffalo and cattle

Mastitis is one of the costliest diseases affecting the world's dairy industry. The important contribution of complement Component 5 (C5) to phagocytosis, which plays a major role in the defence of the bovine mammary gland against infection, makes this component of innate immunity a potential contributor in defending udder against mastitis. The objectives of this study were to sequence and analyse the whole coding region of the C5 gene in Egyptian buffalo and cattle, to detect any nucleotide variations (polymorphisms) and to investigate their associations with milk somatic cell score (SCS) as an indicator of mastitis in dairy animals. We sequenced a buffalo C5 cDNA fragment of 5336 bp (KP221293) and a cattle C5 cDNA fragment of 5303 bp (KP221294), which included the whole coding region and 3-UTR. Buffalo and cattle C5 cDNA shared sequence identity of 99%. The predicted complement C5 proteins consist of 1677 amino acid residues in both animals, one amino acid less than in humans and three amino acids more than in mouse C5 protein. Comparing cDNA sequences of different animals revealed nine novel SNPs in buffalo and seven SNPs in cattle, with two of them being novel. The association analysis revealed that five SNPs in buffalo are highly associated with SCS; indicating the contribution of complement C5 variants in buffalo mastitis resistance. No significant associations were detected between C5 variants and SCS in cattle. This is the first report about C5 variants in buffalo and its association with SCS.

Molecular markers for resistance against infectious diseases of economic importance

Huge livestock population of India is under threat by a large number of endemic infectious (bacterial, viral, and parasitic) diseases. These diseases are associated with high rates of morbidity and mortality, particularly in exotic and crossbred cattle. Beside morbidity and mortality, economic losses by these diseases occur through reduced fertility, production losses, etc. Some of the major infectious diseases which have great economic impact on Indian dairy industries are tuberculosis (TB), Johne's disease (JD), mastitis, tick and tick-borne diseases (TTBDs), foot and mouth disease, etc. The development of effective strategies for the assessment and control of infectious diseases requires a better understanding of pathogen biology, host immune response, and diseases pathogenesis as well as the identification of the associated biomarkers. Indigenous cattle (Bos indicus) are reported to be comparatively less affected than exotic and crossbred cattle. However, genetic basis of resistance in indigenous cattle is not well documented. The association studies of few of the genes associated with various diseases, namely, solute carrier family 11 member 1, Toll-like receptors 1, with TB; Caspase associated recruitment domain 15, SP110 with JD; CACNA2D1, CD14 with mastitis and interferon gamma, BoLA--DRB3.2 alleles with TTBDs, etc., are presented. Breeding for genetic resistance is one of the promising ways to control the infectious diseases. High host resistance is the most important method for controlling such diseases, but till today no breed is total immune. Therefore, work may be undertaken under the hypothesis that the different susceptibility to these diseases are exhibited by indigenous and crossbred cattle is due to breed-specific differences in the dealing of infected cells with other immune cells, which ultimately influence the immune response responded against infections. Achieving maximum resistance to these diseases is the ultimate goal, is technically possible to achieve, and is permanent. Progress could be enhanced through introgression of resistance genes to breeds with low resistance. The quest for knowledge of the genetic basis for infectious diseases in indigenous livestock is strongly warranted.

Genetic mutations potentially cause two novel NCF1 splice variants up-regulated in the mammary gland, blood and neutrophil of cows infected by Escherichia coli

Neutrophil cytosolic factor 1 (NCF1) plays a crucial role in host defense against microbial pathogens. In this study, we investigated the potential alternative splicing patterns, expression and splice-relevant single nucleotide polymorphisms (SNPs) of the bovine NCF1 gene to increase insights into its potential role against bovine mastitis caused by Escherichia coli infection. Using RT-PCR and clone sequencing methods, we found two novel splice variants designed as NCF1-TV1 (retained intron 6) and NCF1-TV2 (retained part of intron 8), respectively, encoding two putative truncated proteins (239AA and 283AA). Two splice variants were drastically up-regulated in the mastitis-infected cows' mammary tissues, blood and neutrophils compared with these of healthy cows using real-time RT-PCR. Genomic sequencing analysis identified four novel SNPs g.10112 G>A, g.10766 T>C, SNPs g.12085 G>A and g.12430 T>C at the ends of intron 6 and intron 8 of NCF1. ESE motif predicted that the SNP (g.10766 T>C) might affect the binding with splicing-related factors and subsequently caused the production of aberrant splice variant NCF1-TV1, which is one of the potential reasons that the functional SNP was associated with increased milk somatic cell score in cow. Our results would help in better understanding the NCF1 gene function in the process against pathogen infection, and the effect of splicing-related SNP on the production of aberrant splice variant and careful functional characterization in dairy cattle.