Part I: The ENCODE Dataset
Part II: Neuroinflammation PET
James L. Kennedy MD, FRCPC, FRSC
Head, Neurogenetics Section,
Director, Neuroscience Research Dept
Centre for Addiction and Mental Health;
Co-Head, Brain and Therapeutics Division,
Professor of Psychiatry and Medical Science,
University of Toronto
With: Sarah Gagliano, Jo Knight, Romina Mizrahi,
Jennie Pouget, Aristotle Voineskos, et al…
International Imaging and Genetics Conference, Irvine, Calif. Jan 22, 2013.
Recent papers (Sept. 2012, Nature)
suggest most DNA is not “junk”
Functional element
A discrete genome segment that
(1) encodes a defined product (e.g. protein, non-coding RNA) or
(2) displays a reproducible biochemical signature
-ie. protein binding (e.g.TFBS) or specific chromatin structure
(e.g. methylation)
Dunham et al. (2012) Nature, 489: 57-74
Chromosome function: folded closed vs open
http://info.med.yale.edu/therarad/glazer/images/chromatin.jpg
Functional elements: Visualize DNA in 3D
10 to 1000 kb
Figure from Ecker et al. (2012) Nature, 489: 52-55
Many assays and methods
to identify functional elements
Histone modifications
DNA methylation sites
Histone-ChIP
RRBS assay
RNA
transcribed
regions
Chromatin structure
& interactions
TFBS
Protein-coding
regions
eg microRNA
Figure adapted from The ENCODE Project Consortium (2011) PloS Biol
Encyclopedia of DNA Elements – ENCODE
Dunham et al, Nature, Sept 6, 2012
“gene desert”
6
ENCODE
Encyclopedia of DNA Elements
Nature ENCODE Explorer
http://www.nature.com/ENCODE
UCSC:
FTP site ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
The ENCODE Project Consortium (2011). A User's Guide to the
Encyclopedia of DNA Elements (ENCODE). PLoS Biol
Visualization on UCSC
http://genome.ucsc.edu/cgi-bin/hgTracks
Prioritization based on functional
annotation
Some gene-prioritization
web tools:
SUSPECT
TOPGENE
POLYSEARCH
GENEDISTILLER
Etc.
How about prioritizing non-coding variants?
Masoudi-Nejad et al. (2012) Mol Genet Genomics, 287:679-698.
Tool to prioritize non-coding
variants: RegulomeDB
variants
score
(rsIDs, VCF files,
BED files, etc.)
http://regulome.stanford.edu/
Boyle, A.P., et al. (2012) Genome Res, 22(9): 1790-1797
Validating the
biology:
SNP Change of
transcription factor
binding site at
cannabis receptor 1
gene (CNR1)
The T but not the C
allele of rs806378
binds the ARNT
transcription factor
Tiwari et al, (2010)
PART 2:
Positron Emission Tomography
(PET) is well suited for synergism
with genetics.
Potkin & Kennedy
1999
Brain Metabolism Following Haloperidol
Treatment by D3 Genotype (FDG n=14)
Gly-Ser
& Ser-Ser
(n=9)
Haloperidol (5wks) Baseline
Baseline
Gly-Gly
(n=5)
(UCI Brain Imaging Centre; Potkin, Basile & Kennedy, 2002)
DRD1, PET FDG, & Clozapine Response
Genotype 2/2
BPRS = 30%
Improvement
Genotype 1/2
BPRS = 7%
Genotype 1/2
Worsening
(Potkin et al, Molec Psychiat 2002)
Translocator Protein 18 kDa
TSPO: mitochondrial role
TSPO modulates ion
transfer eg Ca++, and
some solutes.
Mitochondrial membrane
Consider role in
schizophrenia: oxidation
or inflammation?
TSPO is pleiotropic: oxidation, inflammation, apoptosis
‘TSPO’
TSPO rs6971: Ala/Ala vs Ala/Thr
FEPPA
ligand
binding
to TSPO
High Affinity Binders = Ala/Ala; Mixed Affinity = Ala/Thr
TSPO gene-binding replicates
across other ligands
TSPO - PET Binding
Rough
summary
across 3
studies 
Toronto grp
Innis grp
Rabiner grp
Fully
replicating
100
80
60
40
20
0
TT
TC
CC
Thr/Thr
Ala/Ala
TSPO gene – rs6791 marker
Ala147Thr
SUMMARY

DNA technology moving ahead rapidly
– Next Gen DNA seq, RNA seq, methylome,
and now ENCODE regulatory sites
– Multiple testing & info overload = big
challenges
Genes should link to brain phenotypes
better than to disease (Have we proven this yet??)
 Even a single gene is very complex!
 Candidate genes (eg TSPO) work well
with PET imaging (ligand dictates gene)

How do we find the genes? Will ENCODE
unlock some doors…?
Neurogenetics

Neurogenetics
Section;






& Imaging-Genetics Lab
(Aristotle Voineskos);
Centre for Addiction and
Mental Health, (CAMH);
University of Toronto.
Joanne Knight
Sarah Gagliano
Jennie Pouget
Vanessa Goncalves
Clement Zai
Arun Tiwari
Daniel Mueller
MRI Genetics:
 Tris Lett
 Dan Felsky
PET (TSPO)
 Romina Mizrahi
 Alan Wilson
 Silvain Houle
Supported by Ontario Gov’t; CIHR, BBRF/NARSAD, NIH,