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Consortium of Multiple Sclerosis Centers Annual Symposium
Multiple Sclerosis Genetics A Tale of Two Molecules
Stephen L. Hauser, M.D.University of California, San Francisco
June 1, 2007
Sir Augustus d’Este (1794-1848), from the collection of the Victoria and Albert Museum, London.
Multiple Sclerosis
λλ
Chronic, multifocal CNS disorder
λλ
Immune-mediated myelin destruction
λ
Secondary neurodegeneration
λ
Prevalence has increased
λ
Gender dimorphism
λ
Influence of environment
λ
Racial and familial clustering
λ
Empirically based therapies
Multiple Sclerosis Impediments to Development of Therapies,
Preventions, and Cures
1. Underlying disease heterogeneity
2. Inadequate animal models
3. Uncertain relationship between inflammatory and degenerative stages
4. Limited repertoire of useful biomarkers
5. Very limited knowledge of presymptomatic events and triggers
It is a capital mistake to theorize before one has data. Insensibly one begins to twist facts to suit theories, instead of theories to suit facts. Sherlock Holmes, A Scandal in Bohemia
It is a capital mistake to theorize before one has data. Insensibly one begins to twist facts to suit theories, instead of theories to suit facts.
Sherlock Holmes, A Scandal in Bohemia
Recurrence Rate Estimates for MS
Relationship
Monozygotic twin
Sibling, two affected parentsSibling, one affected parent
Dizygotic twinSiblingParent
Child
Half siblingAunt or uncle
Nephew or niece
Cousin
AdopteeGeneral population
0 5 10 15 20 25 30 35 40
0%
25%
50%
100%
12.5%
Genetic Identity
Age-adjusted lifetime risk
λs =1
λs =190
λs =6.5
λs =20
λs =150
Modified from: Ebers G. et al. Lancet Neurol. 3:104, 2004
Familial Aggregation of MS
1-866-MSGENES
0.0%
1.0%
2.0%
3.0%
4.0%
5.0%
6.0%
7.0%
8.0%
9.0%
10.0%
Alopecia areata Autoimmune hepatitisCrohn's DiseaseUlcerative colitisMeniere's disease MCTDPernicious anemiaPsoriasisRaynaud's phenomenonRheumatoid arthritisSystemic lupus erythematosusGraves' disease/hyperthyroidismHashimoto's thyroiditis/hypothyroiUveitis/iritisAsthmaType 2 DiabetesHeart AttackEmphysema
Autoimmune Disorders in High Risk for MS Families
Barcellos L. et al: Lancet Neurol 5:924, 2006
Disease genes
Genes with rare alleles with strong penetrance and effects (i.e. deletions, expansions, etc.)
Susceptibility genes
Genes with common or rare alleles with weak, but cumulative effects and penetrance and effects (i.e. polymorphisms)
Monogenic disorderMutation
Gene A
Complex disorderGene variations
Gene C
Gene BGene A
Gene D
Mendelian inheritance patterndominant or recessive Complex inheritance pattern
Genetic risk in the population
Impact of mutations/variations in a single gene on disease phenotype
Environment
Post-genomic modifications
Genetic risk in different families
30% AB C
D
Family 2
30%
Family 1
100%
Family 1 Family 2 Family 3
100%
Family 3
Modified from Peltonen & McKusic. Science 291:1224, 2001
Population Sample After Many Generations
Founding Mutation
gene gene
exon
rSNP iSNP cSNP sSNP
amino acidsubstitution
no amino acidsubstitution
Possible phenotype change
(regulatory SNP) (intron SNP)A/A
G/G
A/G
Single Nucleotide Polymorphisms (SNPs)
Haplotype Mapping
• Long-range correlations among SNPS in the human genome organized as haplotype blocks
• The quantum element of genetic variation on a population-wide scale is not the individual base pair or SNP, but rather 5-100 kb blocks of sequence unbroken by recombination in modern human evolution
This suggests that it may be possible to use only a small fraction of the total genetic variation to serve as an adequate test of the remainder
Populations of Mixed Ancestry: African-Americans
• Typical MS does not occur in black Africans • MS occurs in AA but, compared to WA, is less
common, more severe and less responsive to treatment• African chromosomes have a longer population history
(shorter haplotypes) and greater genetic diversity• These features make possible trans-racial comparisons
to define causal genetic variants • Admixture mapping can identify regions of excess
ancestry in the ethnic group at higher risk for a disease
The History of Human Migration
Northern European chromosome
African chromosome
Detecting Admixture Association
Patterson et al. Am J Hum Genet 74: 979, 2004
Putative Disease Locus
100%
50%
0%
20cM 40cM 60cM 80cM 100cM 120cM 140cM
Position on chromosome 19 (centimorgans)
Perc
ent E
urop
ean
Ance
stry
African American Controls
African Americans with MS
International MS Genetics Consortium
LINKAGE ASSOCIATION ADMIXTURE HLA
VanderbiltDuke UCSFMS Genetics Group
Broad
HarvardU. Cambridge
MontrealMinnesotaNS/LIJ Karolinska
Imperial CollegeIMAGEN
Chr1
0.0
1.0
2.0
3.0
Chr2
0.0
1.0
2.0
3.0
Chr3
0.0
1.0
2.0
3.0
Chr4
0.0
1.0
2.0
3.0
Chr5
0.0
1.0
2.0
3.0
Chr7
0.0
1.0
2.0
3.0
Chr8
0.0
1.0
2.0
3.0
Chr9
0.0
1.0
2.0
3.0
Chr10
0.0
1.0
2.0
3.0
Chr11
0.0
1.0
2.0
3.0
Chr12
0.0
1.0
2.0
3.0
Chr13
0.0
1.0
2.0
3.0
Chr15
0.0
1.0
2.0
3.0
Chr16
0.0
1.0
2.0
3.0
Chr17
0.0
1.0
2.0
3.0
Chr18
0.0
1.0
2.0
3.0
Info
Chr19
0.0
1.0
2.0
3.0
Chr20
0.0
1.0
2.0
3.0
Chr21
0.0
1.0
2.0
3.0
Chr22
0.0
1.0
2.0
3.0
ChrX
0.0
1.0
2.0
3.0
Chr14
0.0
1.0
2.0
3.0
Chr6
0.0
2.0
4.0
6.0
8.0
10.0
12.0
cM
Info
International Multiple Sclerosis Genetics Consortium, Am J Hum Genet 77.454-467, 2005
High Density Linkage Screen: 1000 families
HLA
-3-2-10123456789
1-5
1-10
5
1-20
5
2-21
2-12
1
2-22
1
3-61
3-16
1
4-40
4-14
0
5-38
5-13
8
6-30
6-13
0
7-41
7-14
1
8-60
8-16
0
9-88
10-2
2
10-1
22
11-5
6
11-1
56
12-9
9
13-3
3
14-9
14-1
09
15-1
10
16-8
7
17-6
2
18-4
1
19-3
5
20-4
1
21-4
5
X-1
4
X-1
14
Genetic position in centimorgans (Chromosome-Position)
LOD
sco
re(lo
g ba
se 1
0 of
like
lihoo
d)
Chromosome 1 peak
Published scan: 605 cases, 1043 controls
Whole Genome Admixture Scan: African-Americans
-3-2-10123456789
1-5
1-10
5
1-20
5
2-21
2-12
1
2-22
1
3-61
3-16
1
4-40
4-14
0
5-38
5-13
8
6-30
6-13
0
7-41
7-14
1
8-60
8-16
0
9-88
10-2
2
10-1
22
11-5
6
11-1
56
12-9
9
13-3
3
14-9
14-1
09
15-1
10
16-8
7
17-6
2
18-4
1
19-3
5
20-4
1
21-4
5
X-1
4
X-1
14
Genetic position in centimorgans (Chromosome-Position)
LOD
sco
re(lo
g ba
se 1
0 of
like
lihoo
d)
Chromosome 1 peak
Published scan: 605 cases, 1043 controlsCurrent scan: 882 cases, 1056 controls
Whole-Genome Association: 1000 Trios
HLA
HLA
CD25
CD25DBC1
RPL5
ALK
Whole-Genome Replication: 3000 Cases/Controls
0
10
-log1
0(p)
0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300Position
High Density HLA Genotyping: 1000 Triosq p
Class II Class IClass III
0
1
2
3
-log1
0(p)
0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300Position
DRB1*1501 Excluded; (324 Trios)
HLA-CMICA LOC729792
-log1
0(p)
3
10
-log1
0(p)
q p
Class II Class IClass IIID
PB
2D
PB
1D
PA
1
DQ
A
DM
AD
MB
TAP
1
TAP
2D
OB
DR
B1
DR
B5
DR
A
DQ
B1
DQ
A1
LMP
2
LMP
7
Tapa
sin
LTB
TNFa
LTA
C4A
C4B
C2
BF HS
PA
1BH
SP
A1A
HS
PA
1L
HLA
-B
HLA
-C
MIC
-A
MIC
-B
HLA
-E
HLA
-AH
LA-G
HLA
-F
Chromosome 6
MO
G
BTN
PR
L
q p
Class II Class IClass IIID
PB
2D
PB
1D
PA
1
DQ
A
DM
AD
MB
TAP
1
TAP
2D
OB
DR
B1
DR
B5
DR
A
DQ
B1
DQ
A1
LMP
2
LMP
7
Tapa
sin
LTB
TNFa
LTA
C4A
C4B
C2
BF HS
PA
1BH
SP
A1A
HS
PA
1L
HLA
-B
HLA
-C
MIC
-A
MIC
-B
HLA
-E
HLA
-AH
LA-G
HLA
-F
1990s
MO
G
BTN
PR
L
q p
Class II Class IClass IIID
PB
2D
PB
1D
PA
1
DQ
A
DM
AD
MB
TAP
1
TAP
2D
OB
DR
B1
DR
B5
DR
A
DQ
B1
DQ
A1
LMP
2
LMP
7
Tapa
sin
LTB
TNFa
LTA
C4A
C4B
C2
BF HS
PA
1BH
SP
A1A
HS
PA
1L
HLA
-B
HLA
-C
MIC
-A
MIC
-B
HLA
-E
HLA
-AH
LA-G
HLA
-F
2004: African-American genomes
MO
G
BTN
PR
L
q p
Class II Class IClass IIID
PB
2D
PB
1D
PA
1
DQ
A
DM
AD
MB
TAP
1
TAP
2D
OB
DR
B1
DR
B5
DR
A
DQ
B1
DQ
A1
LMP
2
LMP
7
Tapa
sin
LTB
TNFa
LTA
C4A
C4B
C2
BF HS
PA
1BH
SP
A1A
HS
PA
1L
HLA
-B
HLA
-C
MIC
-A
MIC
-B
HLA
-E
HLA
-AH
LA-G
HLA
-F
2007: African-American genomes
MO
G
BTN
PR
L
modifier
q p
Class II Class IClass IIID
PB
2D
PB
1D
PA
1
DQ
A
DM
AD
MB
TAP
1
TAP
2D
OB
DR
B1
DR
B5
DR
A
DQ
B1
DQ
A1
LMP
2
LMP
7
Tapa
sin
LTB
TNFa
LTA
C4A
C4B
C2
BF HS
PA
1BH
SP
A1A
HS
PA
1L
HLA
-B
HLA
-C
MIC
-A
MIC
-B
HLA
-E
HLA
-AH
LA-G
HLA
-F
2007: High resolution mapping
MO
G
BTN
PR
L
protective
modifier
Alaβ71
The Major Genetic Effect on MS Superimposed HLA-DRβ1*1501 and DRβ1*1503 allelic
structures
Allelic and Functional Association of the Interleukin 7 Receptor α
Chain Gene with MS
F3F3
CK
COOHCOOH
α-chain (CD127) IL2R γc -chain (CD132)
Location5p13 humans15 4.6 cM mouse
DistributionThymocytesT, B cellsMonocytesEndothelial cells
SignalingPI3KStat5
JAK1 JAK3
Genomic Conversion Approach to Identify Candidate Genes in MS
Gene Location Number of SNPs
MMP19 12q14 4
CCL2 17q12 5
IL7Rα 5p13.2 (6) 14
SNPselector (Xu et al Bioinformatics 21:4181, 2005) was used to identify SNPs within exons, untranslated and conserved regions within the gene
r 2=0.97
r 2=0.95PDT analysis of IL7R SNPs
760 MS families (197 multi-case families, 1055 MS patients)
SNP Position
(bp)
Minor/majorallele
MAF Gene region
Type Aminoacid
change
OverallPDT p-value
rs13188960* 35889076 T/G 0.24 upstream 0.0023rs7718919 35891753 T/G 0.13 upstream 0.8707rs1389832* 35894478 T/C 0.34 intron 1 0.0804rs1494558* 35896825 A/G 0.34 exon 2 Non-synon. I66T 0.0249rs11567705 35896909 G/C 0.24 intron 2 0.0018rs969128 35896916 G/A 0.13 intron 2 0.9343rs1494555* 35906947 C/T 0.33 exon 4 Non-synon. V138I 0.0327rs7737000 35907030 T/C 0.13 exon 4 Synonymous H165H 0.6801rs1494554* 35909629 C/A 0.29 intron 5 0.7175rs6897932* 35910332 T/C 0.24 exon 6 Non-synon. T244I 0.0006rs987107* 35910984 T/C 0.29 intron 6 0.7856rs987106* 35911350 T/A 0.47 intron 6 0.0134rs3194051* 35912031 G/A 0.29 exon8 Non-synon. I356V 0.7856rs1494571 35915844 C/G 0.28 downstream 0.9276
P-values meeting Bonferroni-corrected significance threshold and respective risk allele are shown in
bold italic. Minor allele frequency (MAF) estimated from genotyped founders. SNPs genotyped by the
HapMap project (http://www.hapmap.org) are denoted with an *.
Replication of the SNP rs6897932 Risk Effect in Independent Datasets
Dataset N P valueUS (familial) 760 (1055 patients) 0.0006
US (c/c) 438/479 0.05
US AA (c/c) 700/300 NS
UK (fam) 1338 trios 0.03
UK-Belgium (c/c) 1077/2725 0.0006
Combined (fam) 2098 0.0001
Combined (White c/c) 1515/3204 0.000005
IL7Ra Alternative Transcripts
Transcripts that include exon 6 membrane bound
Transcripts that exclude exon 6 soluble receptor
rs6897932 T244I locates in exon 6, which codes a trans-membrane domain
The MS associated C allele resulted in a 2 fold increase in skipping exon 6 (more [short product] soluble receptor)
CT T C T C
U DExon 6
DU
B
(326bp)
(232bp)
HeLa cells DT3 cells AT3 cells
0
20
40
60
80
100
T T TC C C
HeLa DT3 AT3
C.
C alleleT allele-RT
20
40
60
80
100
C alleleT allele
Inc
Sk
D
E.
T7 XbaI XhoI
(94bp)(614bp) (573bp)
SP6
pl-11
Pl-11-IL7R382=T
Pl-11-IL7R172=C
or
A
IL7Ra and Homeostatic Control of T-cell Function
IL7Rα
expression by mature T cells is dramatically influenced by extrinsic factors, including cytokines and antigens.
The more receptor a cell expresses, the more signal it receives for survival and proliferation
The more receptor a cell expresses, the more IL7 it consumes, thereby depriving neighboring cells of their survival signals
EBV
MBP
Crossreactive TCR
DRADRB1
DRB5
MBP TCR
CD4+ Treg cell
B7
CD4+
Th1 cell
CTLA4
NK cell
KIR
CD8+
T cell
HLA-C
DRB1*1501 DRB5*0101
HLA-C
APC
Immune Interactions: The Genetic Evidence
IL7RaIL7Ra
IL7Ra
Current Directions
• Most of the MS genome remains unidentified– Collection of larger datasets in progress
• New approaches– Epigenetics– Copy number variation, differential allelic expression – Whole genome sequencing– Biological heterogeneity
• Genotype-phenotype• Pharmacogenomics
• Identify earliest triggering events in individuals at risk for MS
datadatadata
Patient enrollment
Clinical, epidemiologic MRI Genomics Expression
data
Data Integration
The Genetic Multiple Sclerosis Associations Project
HLA DRB1*1501 Influences MRI Lesion Load in Early MS
1.97*1.79*
1.44
Q2/Q1 Q3/Q1 Q4/Q1
DRB1*1501-DRB1*1501+
T2-Lesion Volumes Stratified by Quartiles
Odd
s R
atio
Individuals at Risk for MS The IRIS Study
• A longitudinal study of ~8000 unaffected first degree relatives of new onset MS cases collected across North America, including 900 discordant twins
• Longitudinal surveillance: Genetic markers, Viral responses (e.g. EBNA1); DRB1*1501 restricted T-cell responses to MBP89-96; autoantibodies; neuroimaging
• Goal to identify “preclinical autoimmunity” state prior to MS onset and factors associated with transition to MS
• Primary prevention with vitamin D supplementation?
The UCSF MS Group
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