APOE Final Presentation

8/9/2019 APOE Final Presentation

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APOE AnalysisSharmila Acharya

Dave Hjulberg

William SchuetzRichard SpragueGovindan Subramani

December 6, 2002


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Agenda

Overall approach

SAGE map

Protein structure Organism comparisons

Implications


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Whats special about APOE?

Polymorphic: like eye color, each ofus has one of three common kinds.

Differs by ancestral origin

Affects likelihood of disease

If you have the bad kind, then your oddsof Alzheimers are significantly higher.

If you have the good kind, then enjoy ahigh-fat diet with low risk of heartdisease.


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Overall ApproachNCBI

GooglePubMed OMIM

Literature

What drugs are used?

PDB

LigandDB Protein

Structure

Analysis

Cn3D

Protein Explorer

Accession #:M12529

Protein ID:AAB59518.1

OMIM #:107741

UniGene

OtherOrganisms

SAGE

UniGene

GeneCard

UniGene


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Overview

Three types of human apolipoprotein E (alleles) E2, E3, and E4, encoded by epsilon2, 3, and 4,

respectively.

Epsilon3 is the most common allele (wildtype).

E3 NH2 ---- Cys112 -----Arg158 ---- COOH Epsilon4 differs from epsilon3 by a cys-to-arg

change at position 112 (cys112arg).E4 NH2 ---- Arg112 ------Arg158 -----COOH

Epsilon 2 differs from epsilon3

by a arg-to-cyschange at position 158E2 NH2 ---- Cys112 -----Cys158 -----COOH


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What is Apolipoprotein?

Combine with cholesterol and triglycerols

Apolipoproteins, including APOE,

Help maintain lipoprotein structures Co-factor in lipid metabolism

Act as ligands for lipoprotein receptors

The protein part of fatty proteins. Critical to formation of VLDL and

chylomicrons.


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Alleles: APOE3

Apoe3 most common version

Generally characterized by low incidence

of heart disease 2 major domains

Mutations in the first domain result in APOE2 andAPOE4


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2 Common Mutations

Both are in the Receptor BindingDomain with the "Receptor" being abinding region on the Low Density

Lipoprotein (LDL). The literature suggests that the difference

in the disease-producing ability of the

changed proteins lies in their relativebinding abilities to the Chylomicrons thatclear cholesterol from the blood.


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Alleles: APOE2

Apoe2 homozygotes (having 2 Apoe2 alleles) are morelikely to develop a disease called Type IIIHyperlipoproteinemia, characterized by high bloodplasma cholesterol and triglycerides and an increased

risk of atherosclerosis. But this Apoe2 homozygosity occurs in only about 1% of

the population, and it seems that additional genetic andenvironmental factors are required to develop thedisease.

An extremely low-fat and low-cholesterol diet does notseem to affect the disease, once established.


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Alleles: APOE4

APOE4 amino acid substitution at aminoacid 112

Arginine (positively charged, hydrophillic)instead of cysteine (uncharged, hydrophobic).

Similar to APOE2, a lot-fat diet does not help.


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SAGE Analysis

188 mRNAsequences158 ofthem clustered in 1

UniGene cluster (Hs.169401, apoE), and30 of themunclustered

# Libraries Organ26 Brain

20 mammary gland

16 prostate or ovary

12 colon, pancreas, or

intestine

5 kidney, vascular, or

thalamus


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Collaboration of SAGE Results

Apolipoprotein is synthesized in various organsincluding liver, brain, spleen, and kidney.

Science 1988 Apr 29;244:4852 (622-30)

APOE is expressed at highest levels in liver, with almost nointestinal expression. Brain levels of expression were second only toliver. Adrenal, testis, and ovary also express APOE at lower levels.Treatment with exogenous estradiol caused significant increases inbrain APOE mRNA

(http://www.informatics.jax.org/searches/#Ref_2 3).

Expression in TissuesGenecard


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Expression in Tissues


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Protein Analysis

Method

PDB data viewed through Protein Explorer

Made3

images of each structure (Helices,SpaceFill, and SaltBridges), except for thefragment (which has no salt bridges)

Rotate each image into similar position

Compare


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Lipid Binding and Hydrophobic Clusters

APOE2

APOE3

Helices Salt Bridges


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Protein Structure: APOE3

helices

Salt Bridges

Space fillHelices

http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NFN

http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&db=m&Dopt=b&uid=8756331


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Helices

Salt Bridges

Space fill

http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NFOhttp://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&db=m&Dopt=b&uid=8756331


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Helices

Salt Bridges

Space fill

http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NFOhttp://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&db=m&Dopt=b&uid=8756331


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Ligand Research

APOE is the primary ligand for 2 receptors

Low density lipoprotein (LDL) receptor foundin the liver.

An APOE-specific receptor found in bloodplasma.

In the mutations, the binding capability

may be compromised.


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Organism comparisons

Organism Protein % identity and length

M.musculus:

(mouse)

ref:NP_033826.1 -apolipoprotein E [Musmusculus]

71 % / 315 aa

(see ProtEST )

R.norvegicus:

(rat)

sp:P02650 - APE_RATAPOLIPOPROTEIN EPRECURSOR (APO-E)

69 % / 315 aa

(see ProtEST )

A.thaliana:

(flower)

ref:NP_196392.1 -

putative protein[Arabidopsis thaliana]

28 % / 303 aa

(see ProtEST

D.melanogas

ter:

(fruit fly)

ref:NP_524658.1 -pericardine [Drosophilamelanogaster]

30 % / 305 aa

(see ProtEST )

Tandem repeats in coding regions suggest the gene evolvedthrough duplications of a primordial gene.J Mol Biol 1986; 187:325-40


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Worldwide Phenotypes

APOE2 APOE3 APOE4

Mediterranean 0.04 0.89 0.07

Lapps 0.20 0.31

Khoi San 0.37

Pygmies 0.41

Aborigines (Australia) 0.26

Native Americans 0.00 0.28

Source: OMIM # 107741: Corbo and Scacchi (1999)


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Observations

Craig Ventor of Celera has APOE4

Associated with Alzheimers and Mad Cow

Testing Yourself http://www.bioheartinc.com/biogeno_pricelist_

0700a.html

Will test your APOE e4 alleles for $295.

http://www.genetests.org/ Complete list of labs that test for APOE.

APOE Final Presentation

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