Trinity College Dublin KARI-TRC Shirakawa Institute of Animal Genetics Functional genomics to identify genes and networks influencing survival following Trypanosome challenge.

Functional genomics to identify genes and networks influencing survival following Trypanosome challenge. Shirakawa Institute of Animal Genetics Trinity College Dublin KARI-TRC

Mouse model X = C57BL6 resistant Balb/c susceptible

phenomenology - (1) subjective or phenomenal experience (2) a systematic study of consciousness from a first-person perspective originated by Husserl. See phenomenological critique of representationalism In the philosophy of mind there exists continuing debate about the validity and usefulness of this approach to the study of consciousness. In the philosophy of trypanotolerance …………………..

Trypanotolerance research. 30 years of stamp collecting ?

Studying the tolerant/susceptible phenotype has problems: Separating cause from effect Separating relevant from irrelevant. Dominance of the ‘what is happening to this weeks trendy gene/protein/cytokine?’ approach.

Studying tolerance susceptibility any way has problems: We have no idea of the mechanisms We have no idea of effector tissue (or maybe too many ideas) We have no in vitro model

M. Soller and J.S. Beckmann, FAO Consultation Report, March 1987 ‘Mapping trypanotolerance loci of the N’Dama would allow the rapid introgression of desired traits from other breeds into the N’Dama, while retaining the trypanotolerance traits; or the rapid introgression of the trypanotolerance trait from the N’Dama to other breeds. Mapping of trypanotolerance loci would also be the first step in their eventual cloning and manipulation through genetic engineering techniques’ CCER June 2002

Contribution of 10 genes from Boran and N’Dama cattle to reduction in degree of trypanosomosis Boran (susceptible) N’Dama (tolerant) The N’Dama and Boran each contribute trypanotolerance alleles at 5 of the 10 most significant QTL, indicating that a synthetic breed could have even higher tolerance than the N’Dama.

In mice, we mapped three genomic regions which determine survival time following T. congolense infection D17Mit46 D17Mit16 D5Mit233 D17Mit7 40 D5Mit114 D5Mit24 D1Nds2 MMU17 D1Mit102 80 D1Mit113 D1Mit403 MMU5 MMU1 120cM

The mapping data gives us a point of attack for a functional approach. What are these genes ? How do they affect survival ? What response pathways are common to mouse/cow/human ? What does that tell us about how to survive trypanosome challenge ? The mapping data gives us a point of attack for a functional approach.

Functional genomics technology allows us to look at what genes respond to infection And especially what genes respond differently to infection

Expression analysis of cow and mouse, resistant and susceptible.

Expression analysis of cow and mouse, resistant and susceptible Expression analysis of cow and mouse, resistant and susceptible. Back to stamp collecting?

Expression studies Cow. N’dama vs Boran time course Expression studies Cow N’dama vs Boran time course N’dama x Boran backcross Mouse C57 vs A/J & Balb/c time course C57*A/J congenics (C57*A/J BAC transgenics)

Mouse time course. Liver.

Congenics Lines fixed for alternative ‘alleles’ of each QTL on a susceptible background. Day 0 liver

MMU17 MMU5 MMU1 D17Mit46 D17Mit16 D5Mit233 D17Mit7 40 D5Mit114 D5Mit24 D17Mit46 D17Mit16 D5Mit233 D17Mit7 40 D5Mit114 D5Mit24 D1Nds2 MMU17 D1Mit102 80 D1Mit113 D1Mit403 MMU5 MMU1 120cM

Cxcl1 - inflammatory response

This is NOT a gene hunt! We are trying to understand the biology of the system.

This is NOT a gene hunt! We are trying to understand the biology of the system. But! How do we know when we have the gene we were not looking for?

What to do with candidate genes All the obvious things Plus Exploit the unique populations of cattle ‘Recently’ admixed resistant * susceptible Multiple resistant breeds Multiple resistant species (sheep, goat, wildlife)

Data exchange issues Shirakawa Institute of Animal Genetics Trinity College Dublin KARI-TRC Shirakawa Institute of Animal Genetics Data exchange issues

Shirakawa Institute of Animal Genetics Trinity College Dublin KARI-TRC