Comparative gene expression profiling of milk somatic cells of Sahiwal cattle and Murrah buffaloes.

India is the world's largest milk producing country because of massive contribution made by cattle and buffaloes. In the present investigation, comprehensive comparative profiling of transcriptomic landscape of milk somatic cells of Sahiwal cattle and Murrah buffaloes was carried out. Genes with highest transcript abundance in both species were enriched for biological processes such as lactation, immune response, cellular oxidant detoxification and response to hormones. Analysis of differential expression identified 377 significantly up-regulated and 847 significantly down-regulated genes with fold change >1.5 in Murrah buffaloes as compared to Sahiwal cattle (padj <0.05). Marked enrichment of innate and adaptive immune response related GO terms and higher expression of genes for various host defense peptides such as lysozyme, defensin ß and granzymes were evident in buffaloes. Genes related to ECM-receptor interaction, complement and coagulation cascades, cytokine-cytokine receptor interaction and keratinization pathway showed more abundant expression in cattle. Network analysis of the up-regulated genes delineated highly connected genes representing immunity and haematopoietic cell lineage (CBL, CD28, CD247, PECAM1 and ITGA4). For the down-regulated dataset, genes with highest interactions were KRT18, FGFR1, GPR183, ITGB3 and DKK3. Our results lend support to more robust immune mechanisms in buffaloes, possibly explaining lower susceptibility to mammary infections as compared to cattle.

Milk somatic cell derived transcriptome analysis identifies regulatory genes and pathways during lactation in Indian Sahiwal cattle (Bos indicus).

BACKGROUND: The present study is an effort to understand the genomic drivers of lactation in Sahiwal (Bos indicus), the best milch cattle breed of the tropics. METHODS: RNA sequencing of four animals from early, mid and late lactation stages was performed using milk somatic cells as source of RNA. RESULTS: The genes encoding the milk casein and whey proteins showed highest expression in early and mid lactation, with a declining trend towards the late stage. The enhanced expression of PLIN2, FABP5 and FABP3 genes in mid lactation suggests enrichment of the PPARα pathway which is linked to fatty acid metabolism. A gradual decline in the percentage of genes involved in metabolism of proteins, mRNA and insulin synthesis from early to late lactation reflected transition from lactogenesis to involution. Major biological pathways maintained throughout lactation were adaptive immune system, FGF signaling, EGFR signaling, activated TLR4 signaling, NFkB and MAP kinases activation mediated by TLR4 signaling repertoire. Differential expression analysis revealed 547, 1010 and 1313 differentially expressed genes (p < 0.05) between early-late, early-mid and mid-late stages, respectively. The topmost regulatory genes identified by network analysis from the differentially expressed genes, were involved in Chemokine receptor, GPCR and EGFR1 pathways. CONCLUSION: The genes and pathways delineated in this study have regulatory implications in cell morphogenesis, lipid droplet formation and protein synthesis in the course of lactation. The study provides an insight into the expression profile of genes influencing milk properties and lactation in Sahiwal cattle.

Transcriptome profiling of longissimus thoracis muscles identifies highly connected differentially expressed genes in meat type sheep of India.

This study describes the muscle transcriptome profile of Bandur breed, a consumer favoured, meat type sheep of India. The transcriptome was compared to the less desirable, unregistered local sheep population, in order to understand the molecular factors related to muscle traits in Indian sheep breeds. Bandur sheep have tender muscles and higher backfat thickness than local sheep. The longissimus thoracis transcriptome profiles of Bandur and local sheep were obtained using RNA sequencing (RNA Seq). The animals were male, non-castrated, with uniform age and reared under similar environment, as well as management conditions. We could identify 568 significantly up-regulated and 538 significantly down-regulated genes in Bandur sheep (p≤0.05). Among these, 181 up-regulated and 142 down-regulated genes in Bandur sheep, with a fold change ≥1.5, were considered for further analysis. Significant Gene Ontology terms for the up-regulated dataset in Bandur sheep included transporter activity, substrate specific transmembrane, lipid and fatty acid binding. The down-regulated activities in Bandur sheep were mainly related to RNA degradation, regulation of ERK1 and ERK2 cascades and innate immune response. The MAPK signaling pathway, Adipocytokine signaling pathway and PPAR signaling pathway were enriched for Bandur sheep. The highly connected genes identified by network analysis were CNOT2, CNOT6, HSPB1, HSPA6, MAP3K14 and PPARD, which may be important regulators of energy metabolism, cellular stress and fatty acid metabolism in the skeletal muscles. These key genes affect the CCR4-NOT complex, PPAR and MAPK signaling pathways. The highly connected genes identified in this study, form interesting candidates for further research on muscle traits in Bandur sheep.

Buffalo milk transcriptome: A comparative analysis of early, mid and late lactation.

The expression of genes and their regulation during lactation in buffaloes remains less understood. To understand the interplay of various genes and pathways, the milk transcriptome from three lactation stages of Murrah buffalo was analyzed by RNA sequencing. The filtered reads were mapped to the Bubalus bubalis as well as Bos taurus reference assemblies. The average mapping rate to water buffalo and Btau 4.6 reference sequence, was 75.5% and 75.7% respectively. Highly expressed genes (RPKM > 3000), throughout lactation included CSN2, CSN1S1, CSN3, LALBA, SPP1 and TPT1. A total of 12833 transcripts were common across all the stages, while 271, 205 and 418 were unique to early, mid and late lactation respectively. Majority of the genes throughout lactation were linked to biological functions like protein metabolism, transport and immune response. A discernible shift from metabolism in early stage to metabolism and immune response in mid stage, and an increase in immune response functions in late lactation was observed. The results provide information of candidate genes and pathways involved in the different stages of lactation in buffalo. The study also identified 14 differentially expressed and highly connected genes across the three lactation stages, which can be used as candidates for future research.

Synergistic association of CYP1A1 polymorphisms with increased susceptibility to squamous cell lung cancer in north Indian smokers.

OBJECTIVES: Studies in different populations have shown that polymorphisms within the CYP1A1 gene play an important role in determining individual susceptibility to lung cancer. However, the data obtained so far have been contradictory within the same or different populations. Few studies have focused on the synergistic effect of CYP1A1 polymorphisms on the susceptibility to lung cancer overall and to different histological subtypes along with the impact of smoking. METHODS: A total of 704 individuals (353 lung cancer patients and 351 controls) were evaluated for CYP1A1 polymorphisms. CYP1A1 genotyping was done by means of PCR-RFLP. RESULTS: A CYP1A1 mutant genotype was found to be significantly associated with lung cancer (OR = 3.15; 95% CI = 1.75-5.71; p = 0.0001) and this risk was 4-fold higher in case of squamous cell carcinoma (SCC). The CYP1A1 m2 allelic variant was found to be strongly associated with the risk of SCC and adenocarcinoma. The combined "at risk" genotypes of the CYP1A1 m1 and m2 allelic variants were associated with lung cancer risk and this risk was higher in case of SCC (OR = 2.0; 95% CI = 1.97-3.81; p = 0.028). Furthermore, the lung cancer risk was associated with smoking, especially in heavy smokers carrying CYP1A1 variant genotypes. We also observed that heavy smokers with the mutant m1 genotype were at increased risk of SCC (OR = 5.4; 95% CI = 2.4-11.9; p<0.0001). Furthermore, when stratified for smoking dose and histology, the effect was compounded in heavy smokers and SCC (OR = 7.5; 95% CI = 1.8-30.9; p = 0.004). CONCLUSIONS: Polymorphism in the CYP1A1 gene is an important risk modifier for lung cancer.