Transcript N`Dama (tolerant) - Centre for Genomic Research

Functional genomics to identify genes
and networks influencing survival
Shirakawa Institute of
Animal Genetics
following Trypanosome challenge.
Trinity College
Dublin
KARI-TRC
Functional genomics to identify genes
and networks influencing survival
Shirakawa Institute of
Animal Genetics
following Trypanosome challenge.
Trinity College
Dublin
KARI-TRC
Mouse model
C57BL6 resistant
X
=
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
N’Dama (tolerant)
Boran (susceptible)
15
10
5
0
-5
-10
-15
15
10
5
0
-5
-10
-15
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
0
D17Mit46
D17Mit16
D5Mit233
D17Mit7
40
D5Mit114
D5Mit24
D1Nds2
MMU17
D1Mit102
80
D1Mit113
MMU5
120cM
D1Mit403
MMU1
•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.
Back to stamp collecting?
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
Response of Congenic mice to T. congolense infection
120
100
% surviving
80
60
Tir1AA
Tir1CC
Tir2AA
Tir2CC
Tir3AA
Tir3CC
TirnAA
40
20
(n
(n
(n
(n
(n
(n
(n
= 20)
= 25)
= 60)
= 120)
= 20)
= 90)
= 100)
0
0 - 10
11 - 20
21-30
31-40
41-50
Days post intection
51-60
61-70
71-80
chromosome 1
4
3.5
3
2.5
2
1.5
1
0.5
0
abs_(_cc-aa_)
0
50000000 10000000 15000000 20000000
0
0
0
Chr 4
4
3.5
3
2.5
2
1.5
1
0.5
0
abs_(_cc-aa_)
0
50000000 10000000 15000000 20000000
0
0
0
chr 5
4
3.5
3
2.5
2
abs_(_cc-aa_)
1.5
1
0.5
0
0
50000000 100000000 150000000 200000000
Chromosome 17
4
3.5
3
2.5
2
abs_(_cc-aa_)
1.5
1
0.5
0
0
20000000
40000000
60000000
80000000
0
D17Mit46
D17Mit16
D5Mit233
D17Mit7
40
D5Mit114
D5Mit24
D1Nds2
MMU17
D1Mit102
80
D1Mit113
MMU5
120cM
D1Mit403
MMU1
chr 5
4
3.5
3
Cxcl1 - inflammatory
response
2.5
2
1.5
1
0.5
0
0
50000000 100000000 150000000 200000000
abs_(_cc-aa_)
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
Trinity College
Dublin
KARI-TRC