Membership in high-risk genetic groups predicts Alzheimer’s

disease and age-at-onset

• Elizabeth Corder Duke University

• Shirley Poduslo Medical College of Georgia

APOE is a potential susceptibility gene for AD

APOE alleles and isoforms

G A TC G G C G C G C G CG C

Asp Val Arg Gly Arg

GA TC G G C G G CC

Gln Lys Arg Leu Ala

A A C A

C

3’G A TC G G C G C G C G CG C

Asp Val Arg Gly Arg

GA TC G G C G G CC

Gln Lys Arg Leu Ala

A A C A

112 158 APOE 4

Apo E4

G A TC G G T G C G C G CG C

Asp Val Cys Gly Arg

GA TC G G C G G CC

Gln Lys Arg Leu Ala

A A C A

C

3’G A TC G G T G C G C G CG C

Asp Val Cys Gly Arg

GA TC G G C G G CC

Gln Lys Arg Leu Ala

A A C A

112 158 APOE 3

Apo E3

G A TC G G T G C G C G CG C

Asp Val Cys Gly Arg

GA TC G G C G G CC

Gln Lys Cys Leu Ala

A A T A

C

3’G A TC G G T G C G C G CG C

Asp Val Cys Gly Arg

GA TC G G C G G CC

Gln Lys Cys Leu Ala

A A T A

APOE 2

Apo E2

112 158

APOE genotypes: APOE 2 / 2 APOE 3 / 2

APOE 3 / 3 APOE 4 / 2APOE 4 / 4 APOE 4 / 3

APOENone 20 % 1.0 84 years

One 47 % 2.8 75 years

Two 91% 8.1 68 years

APOE 4 is a susceptibility gene for AD

234 individuals 60 - 94 years of age:

Science 1993

APOE 4 Percent Risk Age at onsetwith AD

Background

• Some degree of AD brain changes (plaques and tangles) is almost universal by age 80

• Extended longevity implies a strong! need to identify root causes and interventions

• I believe that risk pertains to many genes that have biologic plausibility but have been difficult to verify from sample to sample due to wide variation in frequencies of high-risk combinations

Goal

• Use GoM to define multilocus genotypes at high and low risk for AD

• Demonstrate that persons with high resemblance to high-risk ‘pure types’ are affected while those with low membership are OK

Grade of Membership analysis(Woodbury et al., 1978)

• Lambda coefficient (): probability that a specific variable outcome is associated with a particular pure type

• Grade of membership coefficients (gik): estimate the

degree to which a subject belongs to a pure type

Pij gikkj

k

• Internal variables and external (validating) variables

• The number of pure types that provide the best partition of the data matrix is determined by log likelihood tests

Data

• Age/ AD status• APOE genotype• Genotypes for plausible candidate loci:

– APOE promoter polymorphisms at –491 and –427

– Adjacent gene APOCI

– LDL receptor for APOE

– Cystatin C

– Cathepsin D

Table 1. Probabilities representing GoM groups I Table 1. Probabilities representing GoM groups I to V.*to V.*

  

Attribute I II III IV V HAttribute I II III IV V H

AD case 100 100 100 0 0 0.68AD case 100 100 100 0 0 0.68

  

Age (years)Age (years)

< 65 31 17 12 0 0< 65 31 17 12 0 0 0.90 0.90

65- 69 30 0 0 065- 69 30 0 0 0

70 0 45 41 41 070 0 45 41 41 0

75 0 0 36 59 075 0 0 36 59 0

80+ 0 0 0 0 10080+ 0 0 0 0 100

  

Group V: Long life without AD

• Permissive promotion of the APOE gene

• Several genotypes: 23, 33 and even 34!

• Heterozygosity for the LDL receptor for APOE

Table 1.contTable 1.cont

I II III IV V HI II III IV V H

APOE APOE

23 40 0 4 0 48 1.1723 40 0 4 0 48 1.17

33 0 0 0 33 0 0 0 100100 2424

24 47 7 0 0 024 47 7 0 0 0

34 0 0 34 0 0 9696 0 28 0 28

44 19 93 0 0 044 19 93 0 0 0

  

APOE –491APOE –491

AA 0 100 100 100 0 0.90AA 0 100 100 100 0 0.90

AT 0 0 0 0 AT 0 0 0 0 100100

TT 100 TT 100 0 0 0 0 0 0 0 0

  

APOE-427APOE-427

TT 0 100 99 100 74TT 0 100 99 100 74 0.30 0.30

TC TC 100100 0 0 0 25 0 0 0 25

CC 0 0 1 0 1CC 0 0 1 0 1

  

APOCI APOCI

AA n/a 100 0 0 0 0.91AA n/a 100 0 0 0 0.91

AB n/a 0 AB n/a 0 100100 0 100 0 100

BB n/a 0 0 BB n/a 0 0 100100 0 0

  

I II III IV V HI II III IV V H

LDLr8 LDLr8

GG 100 100 100 99 0 0.40GG 100 100 100 99 0 0.40

AG 0 0 0 0 100 AG 0 0 0 0 100

AA 0 0 0 1 0AA 0 0 0 1 0

  

LDLr13LDLr13

TT 0 TT 0 100100 0 0 0 0.82 0 0 0 0.82

TC 0 0 100 53 100TC 0 0 100 53 100

CC 100 0 0 47 0CC 100 0 0 47 0

  

CST3CST3

GG 0 90 84 100 69GG 0 90 84 100 69 0.52 0.52

GA GA 100100 0 0 0 0 0 0 0 0

AA 0 10 16 0 31AA 0 10 16 0 31

  

CTSDCTSD

CC 0 100 100 100 100 0.41CC 0 100 100 100 100 0.41

CT CT 100100 0 0 0 0 0 0 0 0

Group I: Affected before age 70

• Ultra-high expression of APOE

• High-risk homozygous combinations of APOE & LDL receptor genotypes

• Rare cathepsin D + cystatin C genotypes => that slow rate of amyloid degradation

Group II: Affected before age 75

• High-risk APOE44 in combination with an alternate homozygous LDL exon 13 receptor genotypes, I.e. several high-risk APOE-LDL combinations

Group III: Affected before age 80

• Common garden variety APOE34

• Unaffected group IV of similar age carried APOE33 not APOE34

Table 2. AD status according to membership in the high-risk groups (I+II+III)

 AD Membership

0-20% 20-40% 40-60% 60-80% 80-100%

YES (n=180) 0(0%) 11(31%) 43(61%) 24(57%) 102(100%)

NO (n=120) 50(100%) 24(69%) 28(39%) 18(43%) 0(0%)

50 35 71 42 102

Conclusions

• Identification of high-risk combinations of gene variants jointly with the resemblance of study subjects to the to combinations may prove to be useful: – To predict the level of risk and likely age at onset of

AD for individuals– Robust verification of candidate risk genes (the

frequency of high-risk persons may vary from sample to sample while the risk groups rooted in biology are stable)