Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

status: publishe

The First-Generation Whole-Genome Radiation Hybrid Map in the Horse Identifies Conserved Segments in Human and Mouse Genomes

A first-generation radiation hybrid (RH) map of the equine (Equus caballus) genome was assembled using 92 horse × hamster hybrid cell lines and 730 equine markers. The map is the first comprehensive framework map of the horse that (1) incorporates type I as well as type II markers, (2) integrates synteny, cytogenetic, and meiotic maps into a consensus map, and (3) provides the most detailed genome-wide information to date on the organization and comparative status of the equine genome. The 730 loci (258 type I and 472 type II) included in the final map are clustered in 101 RH groups distributed over all equine autosomes and the X chromosome. The overall marker retention frequency in the panel is ∼21%, and the possibility of adding any new marker to the map is ∼90%. On average, the mapped markers are distributed every 19 cR (4 Mb) of the equine genome—a significant improvement in resolution over previous maps. With 69 new FISH assignments, a total of 253 cytogenetically mapped loci physically anchor the RH map to various chromosomal segments. Synteny assignments of 39 gene loci complemented the RH mapping of 27 genes. The results added 12 new loci to the horse gene map. Lastly, comparison of the assembly of 447 equine genes (256 linearly ordered RH-mapped and additional 191 FISH-mapped) with the location of draft sequences of their human and mouse orthologs provides the most extensive horse–human and horse–mouse comparative map to date. We expect that the foundation established through this map will significantly facilitate rapid targeted expansion of the horse gene map and consequently, mapping and positional cloning of genes governing traits significant to the equine industry. [Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: R. Brandon, G. Lindgren, and I. Tammen.

A GPBAR1 (TGR5) small molecule agonist shows specific inhibitory effects on myeloid cell activation in vitro and reduces experimental autoimmune encephalitis (EAE) in vivo.

GPBAR1 is a G protein-coupled receptor that is activated by certain bile acids and plays an important role in the regulation of bile acid synthesis, lipid metabolism, and energy homeostasis. Recent evidence suggests that GPBAR1 may also have important effects in reducing the inflammatory response through its expression on monocytes and macrophages. To further understand the role of GPBAR1 in inflammation, we generated a novel, selective, proprietary GPBAR1 agonist and tested its effectiveness at reducing monocyte and macrophage activation in vitro and in vivo. We have used this agonist, together with previously described agonists to study agonism of GPBAR1, and shown that they can all induce cAMP and reduce TLR activation-induced cytokine production in human monocytes and monocyte-derived macrophages in vitro. Additionally, through the usage of RNA sequencing (RNA-Seq), we identified a select set of genes that are regulated by GPBAR1 agonism during LPS activation. To further define the in vivo role of GPBAR1 in inflammation, we assessed GPBAR1 expression and found high levels on circulating mouse monocytes. Agonism of GPBAR1 reduced LPS-induced cytokine production in mouse monocytes ex vivo and serum cytokine levels in vivo. Agonism of GPBAR1 also had profound effects in the experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis, where monocytes play an important role. Mice treated with the GPBAR1 agonist exhibited a significant reduction in the EAE clinical score which correlated with reduced monocyte and microglial activation and reduced trafficking of monocytes and T cells into the CNS. These data confirm the importance of GPBAR1 in controlling monocyte and macrophage activation in vivo and support the rationale for selective agonists of GPBAR1 in the treatment of inflammatory diseases

GPBAR1 agonism reduces EAE disease severity.

<p>(A) EAE clinical scores are shown for both vehicle and BIX02694 groups (n = 10 mice per group). (B) Cell counts of CNS immune cells assessed on day 13 post-immunization are shown (n = 5 mice). (C) Percentages of blood monocytes (n = 5) or (C) lymphocytes (n = 5) are shown for naive mice (n = 8), along with EAE mice treated with either vehicle or BIX02694. Protein expression of activation markers on both CNS-infiltrating monocytes (E) and microglia (F) are shown (n = 5 mice per group). (G) Protein expression of activation markers on blood monocytes from EAE mice treated with either vehicle or BIX02694 (n = 5 mice per group).</p

Mouse monocytes express GPBAR1 and its agonism reduces LPS-induced cytokine production.

<p>(A) <i>Gpbar1</i> and <i>18s</i> mRNA levels were assessed by Taqman in C57BL/6 mouse whole blood and isolated leukocytes (n = 2 for leukocytes, n = 5 for blood). (B–C) GPBAR1 protein levels were assessed on mouse blood cells by flow cytometry using CD115 to stain monocytes. (B) Gating scheme and representative histograms of lymphocytes, granulocytes and monocytes are shown (n = 1 is shown, representative of 3 mice). (C) Median fluorescence intensity of GPBAR1 on monocytes, granulocytes, and lymphocytes is shown (n = 3, averaged). Monocytes stained with an isotype control are the control sample (B) and (C). (D–F) Impact of GPBAR1 agonism on LPS induced cytokines. Blood from C57BL/6 mice (n = 5, averaged) was stimulated ex vivo with 100 ng LPS in the presence of BIX02694 and intracellular TNFα in monocytes was measured by flow cytometry (D). Balb/c mice were challenged with 2 µg LPS, in the presence of vehicle, Prednisolone (3 mg/kg), or BIX02694 (0.3, 3, 10 mg/kg) and serum cytokine levels were measured; TNFα at 1 hour (E) IL-12p40 (F) and CCL2 (G) both at 4 hours post LPS administration.</p