Model organism genetics and
human disease
With an emphasis on…..
APOYG!
Model Organisms
The “Security Council”
1,000 Myr
500 Myr
80 Myr
Human
Biology
Mammalian
Biology
Multicellular
Biology
Unicellular
Biology
Not so many genes!
6,000
14,000
19,000
21,000
Why we love yeast
Model organism
Eukaryotic intracellular biology
Gene function conservation
(e.g., human disease genes)
Testbed for genomic technologies
Experimental approaches
Classical genetics (+biochemistry)
Recombinant genetics
Emerging technologies
Community of “yeast people”
Open exchange of ideas, reagents, results
Collaboration
Saccharomyces cerevisiae
Budding yeast
The “E.coli of eukaryotic cells”
Yeast vs. Human
~50% of yeast genes
have at least one
similar human gene
~50% of human genes
have at least one
similar yeast gene
Human vs. Yeast
Human disease genes in model organisms
Disease
Human Mouse Fruit fly Worm Yeast Bacteria
Ataxia
ATM
MEI-41
T06E4.3 TEL1
telangiectasia ATM
Breast
BRCA1,2 BRCA1,2
cancer
Cystic
CFTR
CFTR
MDR50
mrp-1,2 YCF1
MDL
fibrosis
Duchenne
DMD
SPEC-B F15D3.1a
muscular dys DMD
HNP colon
MSH2
MSH2
SPEL1
msh-2
MSH2 MUTS
cancer
Huntingtin
HD
HD
disease
Werner
syndrome
Wilson
disease
Waardenburg
syndrome
(huntingtin) (huntingtin)
WRN
WRN
MUS309
wrn-1
SGS1
RECQ
WND
ATP7B
CA-P60A
B0365.3
CCC2
f834
PAX3
PAX3
CG6716-P
vab-3
Human disease genes in model organisms
Disease
Human Mouse Fruit fly Worm Yeast Bacteria
Ataxia
ATM
MEI-41
T06E4.3 TEL1
telangiectasia ATM
Breast
BRCA1,2 BRCA1,2
cancer
Cystic
CFTR
CFTR
MDR50
mrp-1,2 YCF1
MDL
fibrosis
Duchenne
DMD
SPEC-B F15D3.1a
muscular dys DMD
HNP colon
MSH2
MSH2
SPEL1
msh-2
MSH2 MUTS
cancer
Huntingtin
HD
HD
disease
Heo et al. (1999) Genes to Cells 4, 619-625.
Werner
syndrome
Wilson
disease
Waardenburg
syndrome
(huntingtin) (huntingtin)
WRN
WRN
MUS309
wrn-1
SGS1
RECQ
WND
ATP7B
CA-P60A
B0365.3
CCC2
f834
PAX3
PAX3
CG6716-P
vab-3
APOYG and Disease: Two examples
Zelwegers Syndrome
Peroxisome biogenesis
Colorectal Cancer
Genome instability
Zellweger Spectrum
Zellweger
syndrome
Neonatal adrenoleukodystrophy
Infantile
Refsum Disease
Zellweger Patient Cells Share a
Common Phenotype with Yeast pex Mutants
Control
Zellweger patient
Wild-type
pex mutant
Human
 PTS1)
Yeast
(PTS1 - GFP)
Strategies for
Mammalian PEX Gene Identification
Functional complementation
Mammalian cDNA expression libraries
“Homology probing”
Identify all yeast peroxins
Identify all homologous human proteins
Test as “candidate genes”
Yeast / Human Connections
Human
Identification
Function
Yeast
Discovery of Yeast and Human PEX Genes
25
Yeast
PEX Genes
20
15
Human
10
5
0
1990
1992
1994
1996
1998
2000
Cancer
C. Rieder
If you want to understand cancer, you need answers
to the many questions about the role genome instability
plays. ---Bert Vogelstein, 2002
Genetic Instability in Human Cancers
MIN: Microsatellite instability
(increased mutation rate)
CIN: Chromosome instability
(increased aneuploidy rate)
Metaphase
Anaphase
Improperly attached
kinetochore
Spindle
Checkpoint
Bub1, Bub3,
Mad1, Mad2, Mad3
Cohesin
Separase
Securin
APCCdc20
~20% of CIN mutational
spectrum in colon cancer
Improperly attached
kinetochore
4%
2%
hBUB1
Spindle
Checkpoint
Bub1, Bub3,
Mad1, Mad2, Mad3
hMRE11
Cohesin
Separase
11%
hCDC4
Securin
hDING
4%
APCCdc20
Yeast as a model
CIN biology (gene function)
CIN candidate genes- (Cancer CIN genes)
Therapeutics
Finding an “Achilles heel” of cancer
What are all the proteins mutable to CIN?
Spontaneous mutants
eg, CTF mutant collection
HieterLab
members (20yrs)
Systematic screening
Karen Yuen
Non-essential D mutants
Ts mutants, semi-permissive Shay Ben-Aroya
Chromosome Transmission Fidelity (ctf) Screen
Colony Sectoring Assay
non-essential Chromosome Fragment
M
SUP11
+
White colony
(10-4)
wt
EMS mutagenesis
ctf mutant
Sectored colony
(10-2)
138 mutants, ~50 genes
Summary of the 26 Cloned ctf Mutants
ctf
1
2
3
4
5
6
7
8
9
10
11
12
18
13
14
15
17
19
s3
s127
s138
s141
s143
s155
s165
s166
# alleles
30
11
11
8
5
5
5
3
3
3
3
3
3
1
1
1
2
2
1
1
1
1
1
1
1
1
Gene Name
CTF1/CHL1
TOF1/CTF2
CTF3
CTF4/CHL15/POB1
CTF5/MCM21
CTF6/RAD61
CTF7/ECO1
CTF8
SMC3/CTF9
CDC6/CTF10
PDS5/CTF11
CTF12/SCC2
CTF18/CHL12
CTF13
CTF14/NDC10
CTF15/RPB4
CTF17/MCM17/CHL4
CTF19
BIM1
SIC1
SPT4
NUP170
MAD1
MCM16
SCC3
SMC1
Essential?
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Function
Cohesion (helicase)
Cohesion, replication
Kinetochore protein
Cohesion (establishment)
Kinetochore protein
Cohesion
Cohesion (establishment)
Cohesion (alternative RFC)
Cohesion (cohesin subunit)
DNA replication
Cohesion (cohesin associated)
Cohesion (cohesin loading)
Cohesion (alternative RFC)
Kinetochore protein (CBF3)
Kinetochore protein (CBF3)
Subunit of RNA polymerase II
Kinetochore protein
Kinetochore protein
Microtubule binding
Cdk inhibitor
Chromatin structure
Nucleoporin
Spindle checkpoint
Kinetochore protein
Cohesion (cohesin subunit)
Cohesion (cohesin subunit)
Kinetochore
proteins
Cohesion
DNA /RNA
metabolism
13 genes
93 / 138
S. cerevisiae Genome Deletion Project
•“Complete” set of yeast nonessential deletion mutants
•~4,700 haploid strains
•~4,700 homozygous diploid strains
nonessential genes deleted with kanMX = fifty 96 well plate
•~5,800 heterozygous diploid strains
96 well plate
frozen glycerol
stock
pin 96 strains
onto G418 plates
condense 4
plates onto 1
The yeast gene knockout collection
Yeast CIN genes
~300 non-essential genes
(85% coverage)
~100 essential genes
(and still counting)
Human homologs?
12 yeast CIN genes have top-hit human homologs that are
mutated in cancers
Gene
Top Human Hit E-value Cancer Type/Cancer syndromes
ADE17
ATIC
RAD54
RAD54L
TPD3
PPP2AR
1E-133 Lungcancer
RAD51
RAD51
1E-122 Susceptibility to breast cancer
RDH54
RAD54B
SGS1
BLM
RAD1
ERCC4
1E-121 Lymphoma,n-Hodgkin; Colonadecarcima
Bloomsyndrome; leukemia, lymphoma, skin squamous cell, other
1E-115
cancers
Xeroderma pigmentosum, groupF; skin basal cell, skin squamous
1E-109
cell, melama
MRE11 MRE11A
DUN1
CHK2
BUB1
BUB1
MAD1
MAD1L
CDC73
parafibromin
0 anaplastic large cell lymphoma
Lymphoma,n-Hodgkin; Breastcancer, invasiveintraductal; Colon
1E-164
adecarcima
1E-108 Ataxia-telangiectasia-like disorder, colorectal cancer with CIN
Li-Fraumeni syndrome; Osteosarcoma, somatic; Prostatecancer,
familial; Susceptibility to breast and colorectal cancer
1E-41 Colorectal cancer with CIN
6E-55
5E-12 Lymphoma, somatic; Prostatecancer, somatic
Hyperparathyroidism-jaw tumor syndrome; Hyperparathyroidism,
9E-12
familial primary; Parathyroid adema with cystic changes
CIN mutational spectrum in cancer- Why?
Cancer biology
Tumor classification
Identification of new drug targets
CIN gene / Synthetic Lethal gene pairs
Synthetic Lethality
yfg2
yfg1
Viable
Yfg2 = Drug target
Yfg1 = CIN mutant
Viable
Normal
yfg2
yfg1
Dead
Tumor
Yeast Genetic Interactions
MRE11
(4%)
BUB1
(2%)
12 yeast CIN genes have human homologs that are mutated
in cancers
Gene
Top Human Hit E-value Cancer Type/Cancer syndromes
ADE17
ATIC
RAD54
RAD54L
TPD3
PPP2AR
1E-133 Lungcancer
RAD51
RAD51
1E-122 Susceptibility to breast cancer
RDH54
RAD54B
SGS1
BLM
RAD1
ERCC4
1E-121 Lymphoma,n-Hodgkin; Colonadecarcima
Bloomsyndrome; leukemia, lymphoma, skin squamous cell, other
1E-115
cancers
Xeroderma pigmentosum, groupF; skin basal cell, skin squamous
1E-109
cell, melama
MRE11 MRE11A
DUN1
CHK2
BUB1
BUB1
MAD1
MAD1L
CDC73
parafibromin
0 anaplastic large cell lymphoma
Lymphoma,n-Hodgkin; Breastcancer, invasiveintraductal; Colon
1E-164
adecarcima
1E-108 Ataxia-telangiectasia-like disorder, colorectal cancer with CIN
Li-Fraumeni syndrome; Osteosarcoma, somatic; Prostatecancer,
familial; Susceptibility to breast and colorectal cancer
1E-41 Colorectal cancer with CIN
6E-55
5E-12 Lymphoma, somatic; Prostatecancer, somatic
Hyperparathyroidism-jaw tumor syndrome; Hyperparathyroidism,
9E-12
familial primary; Parathyroid adema with cystic changes
Yeast CIN Genes and Human Cancer
CIN “candidate genes”
Somatic mutations in colon cancer
~40% spectrum in 11 genes
Cancer therapeutics
“Achilles heel” candidate genes
Validation in mammalian cells
Four volumes of
the Encyclopedia of Life
6000 14,000 19,000 21,000
April, 1953
April, 2003
Human genome
sequence “completed”
~10,000 parts
~6,000 genes
~4,000,000 parts
~20,000 genes
Power of Model Organism Research
Genetics, biochemistry, genomics
Basic biology
Human health
Human disease
Therapy
Preventative medicine
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