Using mouse genetics to understand human disease

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Using mouse genetics to understand human disease
Mark Daly Whitehead/Pfizer Computational
Biology Fellow
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What we do

• Genetics the study of the inheritance of
  biological phenotype
• Mendel recognized discrete units of inheritance
• Theories rediscovered and disputed ca. 1900
• Experiments on mouse coat color proved Mendel
  correct and generalizable to mammals
• We now recognize this inheritance as being
  carried by variation in DNA

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Why mice?
What do they want with me?

• Mammals, much better biological model
• Easy to breed, feed, and house
• Can acclimatize to human touch
• Most important we can experiment in many ways
  not possible in humans

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Mice are close to humans
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Kerstin Lindblad-Toh Whitehead/MIT Center for
Genome Research
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Mouse sequence reveals great similarity with the
human genome
Extremely high conservation 560,000 anchors
Mouse-Human Comparison both genomes 2.5-3
billion bp long 99 of genes have homologs
95 of genome syntenic
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Genomes are rearranged copiesof each other
Roughly 50 of bases change in the evolutionary
time from mouse to human
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Mouse sequence reveals great similarity with the
human genome
Extremely high conservation 560,000 anchors
Anchors (hundreds of bases with 90
identity) represent areas of evolutionary
selection but only 30-40 of the highly
conserved segments correspond to exons of genes!!!
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What we can do
YIKES!!!

• Directed matings
• Inbred lines and crosses
• Knockouts
• Transgenics
• Mutagenesis
• Nuclear transfer
• Control exposure to pathogens, drugs, diet, etc.

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Example diabetes related miceavailable from The
Jackson Labs

• Type I diabetes (3)
• Type II diabetes (3)
• Hyperglycemic (27)
• Hyperinsulinemic (25)
• Hypoglycemic (1)
• Hypoinsulinemic (5)
• Insulin resistant (30)

• Impaired insulin processing (7)
• Impaired wound healing (13)

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Inbreeding

• Repeated brother-sister mating leads to
  completely homozygous genome no variation!

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Experimental Crosses

• Breed two distinct inbred lines
• Offspring (F1) are all genetically identical
  they each have one copy of each chromosome from
  each parent
• Further crosses involving F1 lead to mice with
  unique combinations of the two original strains

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Experimental Cross
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Experimental Cross backcross

• F1 bred back to one of the parents
• Backcross (F1 x RED) offspring
• 50 red-red
• 50 red-blue

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Experimental Cross F2 intercross

• One F1 bred to another F1
• F2 intercross (F1xF1) offspring
• 25 red-red
• 50 red-blue
• 25 blue-blue

F2
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Trait mapping
100 200 300
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Trait mapping
Blue trees tall, Red trees short In the F2
generation, short trees tend to carry red
chromosomes where the height genes are located,
taller trees tend to carry blue chromosomes
QTL mapping use statistical methods to find
these regions
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How do we distinguish chromosomes from different
strains?

• Polymorphic DNA markers such as Single Nucleotide
  Polymorphisms (SNPs) can be used to distinguish
  the parental origin of offspring chromosomes

ATTCGACGTATTGGCACTTACAGG ATTCGATGTATTGGCACTTACAGG
SNP
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Example susceptibility to Tb

• C3H mice extremely susceptible to Tb
• B6 mice resistant
• F1, F2 show intermediate levels of susceptibility

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One gene location already known

• Previous work identified chromosome 1 as carrying
  a major susceptibility factor
• Congenic C3H animals carrying a B6 chromosome 1
  segment were bred

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Congenic and consomic mice

• Derived strains of mice in which the homozygous
  genome of one mouse strain has a chromosome or
  part of a chromosome substituted from another
  strain

C3H B6
C3H.B6_chr1
Chr 1 Chr 2 Chr 3 Chr 4 Etc.
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Tb mapping cross
F2 intercross C3H.B6-sst1 - MTB-susceptible,
carrying B6 chr 1 resistance B6 -
MTB-resistant Trait survival following MTB
infection
x
B6
C3H.B6-sst1
x
F1

F2
n 368
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Results 3 new gene locations identified!
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Gene identified on chromosome 12
At the end of chr 12 mice inheriting two C3H
copies survive significantly longer than those
with one or two B6 copies Mice engineered to
be missing a critical component of the immune
system located in this region are likewise more
susceptible, validating that particular gene as
involved in Tb susceptibility
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Mouse History

• Modern house mice emerged from Asia into the
  fertile crescent as agriculture was born

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Mouse history
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Recent mouse history
Fancy mouse breeding - Asia, Europe (last few
centuries) Retired schoolteacher Abbie
Lathrop collects and breeds these mice Granby, MA
1900 Castle, Little and others form most
commonly used inbred strains from Lathrop
stock (1908 on)
W.E. Castle C.C. Little
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Mouse history
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Mouse history

• Asian musculus and European domesticus mice
  dominate the world but have evolved separately
  over 1 Million years
• Mixing in Abbie Lathrops schoolhouse created all
  our commonly used mice from these two distinct
  founder groups

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Genetic Background of the inbred lab mice
C57BL/6
musc
musc
domest
musc
domest
domest
C3H

musc
domest
domest
DBA
cast
Avg segment size 2 Mb
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Comparing two inbred strains frequency of
differences in 50 kb segments


40 SNP/10 kb
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Finding the genes responsible for biomedical
phenotypes
C3H (susceptible) B6 (resistant)
Traditionally positional cloning is
painful (e.g., generating thousands of mice for
fine mapping, breeding congenics) As a result,
countless significant QTLs have been identified
in mapping crosses but only a small handful have
thusfar resulted in identification of which gene
is responsible the critical information that
will advance research into prevention and
treatment!
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Using DNA patterns to find genes
C3H (susc.) B6 (res.) Critical Region
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Using DNA patterns to find genes
C3H (susc.) B6 (res.) DBA (susc.) Critical Region
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Example mapping of albinism
Critical region
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First genomic region mapped
Chr 4 35.7
37.6 37.9
39.4 (Mb)
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Future Genetic Studies
Mapping
Expression
Pathways
Model Systems
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Thanks to
(Whitehead Institute) Claire Wade Andrew
Kirby (MIT Genome Center) EJ Kulbokas Mike
Zody Eric Lander Kerstin Lindblad-Toh Funding W
hitehead Institute Pfizer, Inc. National Human
Genome Research Institute