Transcriptomic comparison of primary bovine horn core carcinoma culture and parental tissue at early stage

Aim:

Squamous cell carcinoma or SCC of horn in bovines (bovine horn core carcinoma) frequently observed in Bos indicus affecting almost 1% of cattle population. Freshly isolated primary epithelial cells may be closely related to the malignant epithelial cells of the tumor. Comparison of gene expression in between horn’s SCC tissue and its early passage primary culture using next generation sequencing was the aim of this study.

Materials and Methods:

Whole transcriptome sequencing of horn’s SCC tissue and its early passage cells using Ion Torrent PGM were done. Comparative expression and analysis of different genes and pathways related to cancer and biological processes associated with malignancy, proliferating capacity, differentiation, apoptosis, senescence, adhesion, cohesion, migration, invasion, angiogenesis, and metabolic pathways were identified.

Results:

Up-regulated genes in SCC of horn’s early passage cells were involved in transporter activity, catalytic activity, nucleic acid binding transcription factor activity, biogenesis, cellular processes, biological regulation and localization and the down-regulated genes mainly were involved in focal adhesion, extracellular matrix receptor interaction and spliceosome activity.

Conclusion:

The experiment revealed similar transcriptomic nature of horn’s SCC tissue and its early passage cells.

Identification of novel SNPs in differentially expressed genes and its association with horn cancer of Bos indicus bullocks by next-generation sequencing

The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM. Data obtained were analysed using DNASTAR software package and case control analysis using SAS software. We found SNP present in BPIFA1 gene of B. indicus shows association with event of HC which reflects its potential to be a genetic marker. Bioinformatic analysis to detect structural and functional impact nsSNP of BPIFA1 added another layer of confirmation to our result. We successfully identified SNP associated with HC as well as demonstrated efficient approach for limited number of SNP discovery and validation in targeted genomics regions in large number of samples combining PCR amplification and Ion Torrent PGM sequencing which suits small-scale laboratories with limited budget.

Comprehensive transcriptome profiling of squamous cell carcinoma of horn in Bos indicus

Squamous cell carcinoma (SCC) of horn is frequently observed in Bos indicus affecting 1% of cattle population and accounting 83.34% of total tumours found. The transcriptome profile of horn cancer (HC) tissue and the matched normal (HN) tissue were analysed by RNA-seq using Roche 454 sequencing. A total of 1 504 900 reads comprising of 612 MB data were used to identify differentially expressed genes using CLC Genomic Workbench. These include up-regulation of KRT6A, KRT6B, KRT6C, KRT14, SFN, KRT84, PI3, COL17A1, ANLN, SERPINB5 and down-regulation of BOLA, SCGB1A1, CXCL17, KRT19, BPIFB1, NR4A1 and TFF3 in HC, which are involved in regulation of gene transcription, cell proliferation, apoptosis, cell survival and metabolic pathways. The qPCR analysis of several targets suggested concordance of gene expression profile with RNA-seq analysis. The present findings would provide basis for further screening of genes and identification of markers for early diagnosis and therapeutic intervention of HC.

High through put 16S rRNA gene-based pyrosequencing analysis of the fecal microbiota of high FCR and low FCR broiler growers

The performance of birds appears to vary among the flock of growing broilers which may in part be due to variation in their gut microbiota. In the view of poultry industry, it is desirable to minimise such variation. We investigated metagenomic profile of fecal bacteria in birds with high and low feed conversion ratio (FCR) to identify microbial community linked to low and high FCR by employing high throughput pyrosequencing of 16S rRNA genomic targets. Therefore feeding trial was investigated in order to identify fecal bacteria consistently linked with better feed conversion ratio in bird performance as measured by body weight gain. High-throughput 16S rRNA gene based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. The fecal microbial community of birds was predominated by Proteobacteria (48.04 % in high FCR and 49.98 % in low FCR), Firmicutes (26.17 % in high FCR and 36.23 % in low FCR), Bacteroidetes (18.62 % in high FCR and 11.66 % in low FCR), as well as unclassified bacteria (15.77 % in high FCR and 14.29 % in low FCR), suggesting that a large portion of fecal microbiota is novel and could be involved in currently unknown functions. The most prevalent bacterial classes in high FCR and low FCR were Gammaproteobacteria, Clostridia and Bacteroidia. However in low FCR birds Phascolarctobacterium, Faecalibacterium and Clostridium predominated among the Clostridia. In FCR comparison of fecal bacteria, about 36 genera were differentially abundant between high and low FCR birds. This information could be used to formulate effective strategies to improve feed efficiency and feed formulation for optimal gut health.

Metagenomic analysis of virulence-associated and antibiotic resistance genes of microbes in rumen of Indian buffalo (Bubalus bubalis)

A major research goal in rumen microbial ecology is to understand the relationship between community composition and its function, particularly involved in fermentation process is of a potential interest. The buffalo rumen microbiota impacts human food safety as well as animal health. Although the bacteria of bovine rumen have been well characterized, techniques have been lacking to correlate total community structure with gene function. We applied 454 next generations sequencing technology to characterize general microbial diversity present in buffalo rumen metagenome and also identified the repertoire of microbial genes present, including genes associated with antibiotic resistance and bacterial virulence. Results suggest that over six percent (6.44%) of the sequences from our buffalo rumen pool sample could be categorized as virulence genes and genes associated with resistance to antibiotic and toxic compounds (RATC), which is a higher proportion of virulence genes reported from metagenome samples of chicken cecum (5.39%), cow rumen (4.43%) and Sargasso sea (2.95%). However, it was lower than the proportion found in cow milk (11.33%) cattle faeces (8.4%), Antarctic marine derived lake (8.45%), human fecal (7.7%) and farm soil (7.79%). The dynamic nature of metagenomic data, together with the large number of RATC classes observed in samples from widely different ecologies indicates that metagenomic data can be used to track potential targets and relative amounts of antibiotic resistance genes in individual animals. In addition, these data can be also used to generate antibiotic resistance gene profiles to facilitate an understanding of the ecology of the microbial communities in each habitat as well as the epidemiology of antibiotic resistant gene transport between and among habitats.

Milk microbiome signatures of subclinical mastitis-affected cattle analysed by shotgun sequencing

AIMS

Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus × B. indicus) cattle harbouring subclinical mastitis was carried out by next-generation sequencing 454 GS-FLX technology to elucidate the microbial community structure of cattle milk.

METHODS AND RESULTS

Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63·07, 11·09 and 7·87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web-based tool MG-RAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt-zinc-cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed.

CONCLUSIONS

The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows.

SIGNIFICANCE AND IMPACT OF THE STUDY

The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it.