A smattering of mutations
Brainiacs: Recent Advances in Neuroscience
2014 IBBS Science Writer’s Workshop
April 28, 2014
National Press Club, Washington, DC
Aravinda Chakravarti, PhD
Center for Complex Disease Genomics
Johns Hopkins University School of Medicine
Disclosures: Biogen Idec (SAB)
Biology is complicated but
not random
The world of
biology at the
molecular level is
complicated
…not only in the
large number of
components but
in their
interactions,
never mind how
these change with
time, exposure,
etc.
For future understanding of biology we have
to come to grips with complexity…Occam’s
razor rarely applies. So, how can sense be
made of this complexity?...For that we need
to know which parts of the network are at
the heart of the process…Reducing the
elements to the minimum will focus
attention on those that are central to the
process and this should help gain better
understanding.
Paul Nurse
Emerging Themes in Biology: Hints for the Future
Cell, March 27, 2014
Finding “elite” genes for autism:
the roles of delta 2 catenin (CTNND2)
The many genes for autism…
Simons Foundation for
Autism Research, 2014
Genetic Principle #1: Structure begets function
Mutations occur
at random but
those retained
are not…
…our genomes
hold the code to
conservation of
function by
conserving
structure
Genetic Principle #2: Rarer forms of a
disease arise from higher liability
Cedric Carter
Doug Falconer
Sex-Independent
Threshold
Liability = susceptibility + exposure
The more critical the function the more severe the consequences
of its disruption and the greater the effect of natural selection
Female-enriched Multiplex families for
autism (FEMFs)
•
•
•
•
Genetic reasoning (Carter effect) and empirical data
indicate FEMFs should have the highest liability;
An extreme phenotype with incidence <1.6x105…(female patients ~ 0.0016, <10% families are
multiplex, <10% are severe);
ADI-R and ADOS positive cases sampled from the
NIMH and AGRE repositories;
>180 FEMFs being sequenced.
Sequencing FEMFs…a pilot
study
13 FEMFs
71 European controls
•
•
Exome Sequencing
Focus on variants of
interest (VOI)
•
absent in controls
•
functionally deleterious
3,090 VOI in 2,516 Genes
(Autism + 1000 Genomes)
447 Genes with 2+ VOI
(Autism + 1000 Genomes)
In Autism Exomes Only
18 genes which do not show up in
10,000 permutations of European
exomes
ABP1, ATP11A, CTNND2,
CYFIP1, DLG1, ENO1, ITGB5,
MEP1A, MIPEP, MYO1A, MYOF,
PARPBP, PLXNA3, SIAE, TAT,
THBS4, ZBTB39, ZNF192
Amino Acid Changes in CTNND2 (NP_001323)
Potential mutations at CTNND2
Protein Domain
Amino Acid Changes in CTNND2 (NP_001323)
Post−Translational Modification
Amino Acid Changes in CTNND2 (NP_001323)
T862M
R713C
ARM
T862M
T862M
R713C
R713C
●
ARM ARMARM ARM ARM
PDZ
●
●
●
950
1000
1050
1100
1150
1200
950 950
10001000
10501050
11001100
11501150
12001200
PDZ
900
ARM ARMARM ARM ARM
900 900
ARM
850
ARM ARM ARM ARM
850 850
PDZ
800
ARM ARMARM ARM ARM
800 800
ARM
750
ARM ARM ARM ARM
750 750
●
400
●
350
●
700
●
●
●
●
650
●
ARM ARM ARM ARM
600
●
●
●
550
R454H
R454H
G275C
G275C
●
300
250
150
●
700 700
650 650
600 600
550 550
500 500
450 450
400 400
350 350
300 300
200 200
•
150 150
Amino Acid Position
100 100
0
50
0
0.5
50
Conservation
POLYPROLINE
0
0.5
1
CC
0
Conservation
0
0
1
●
EVS
EVS
MAF=0 MAF=0
●
●
POLYPROLINE
100
0.5
●
●
CC
50
Conservation
●
●
●
●
P224LP224L
1
●
●
POLYPROLINE
●
Autism
P189LP189L
CC
●
200
G34SG34S
Autism
●
Q507P
●
Q507P
Q507P
G275C
●
500
P224L
●
●
EVS MAF
< 0.0002
EVS
MAF=0
250 250
Autism
R454H
P189L
●
EVS MAF
< 0.0002
450
G34S
Protein Domain
Post−Translational Modification
Protein Domain
Post−Translational Modification
300 independent autism females
Amino Acid Position
Amino Acid Position
•
5 conserved to zebrafish
•
Autism vs. controls: p=5.26x10-7
CTNND2 mutations are loss-of-function
Deletion
Duplication
Deletions/Duplications Overlapping Exons vs. controls: p=5x10-4
Loss-of-function of CTNND2 in zebrafish
Control variants
look like this
(8-10 somite
stage)
Mutant variants look like these…the greater the
mutant severity the more abnormal the embryos
in number and quality
Autism variants have specific effects on
neuronal function*
Dendritic spines are location of excitatory synaptic transmission
dsRed
GFP
Alone
wildtypeCTNND2
G34S
mutant
R713C
mutant
A482T
polymorphism
A482T
*rat hippocampal neurons
(E18 embryos)
Is there any effect on
behavior?
•
CTNND2 Knockout
mouse: severe synaptic
and cognitive dysfunction
(Israely et al. 2004)
•
Involved in activity related
change in morphology at
the synapse (Kosik et al.
2005)
Israely et al. 2004
What does delta 2 catenin do?
Guilt-by-association: which genes are expressed with CTNND2?
Allen Brain Atlas: 28 developmental time-points
Negatively Correlated
662 genes
Cell Cycle
(in particular, mitosis)
Positively Correlated
826 genes
Morphogenesis, projection
formation, and neuron
differentiation
B.
FEZF2
HERC2
HDAC3
LR S
NF RC
SA IA 7
MA TB
AS P2 2
FE TN
SD ZF2 2
PP K1
GP P1R
SL R37 1B
C
EM 24
NR L1 A2
AP CA
SO C M
TH X
CT RA 5
BZ TNB
RP RA P2
DL S6 P1
SY G4 KA2
BI T3
DP N1
SH P6
A
ZN N
KI F82 K1
SN F5C 7
CA X19
SB C
CD F1 NA1
H
FG KL
YE D1 5
AR A T
SH ID1 S2
AD AN B
MB CY5 K2
A D5
A TXN
KL UTS 7
G C2 2
ZN RIN2
TS F8 B
C
HE 1
PO RC
ME GZ 2
D
D 1
CM AG 2
AN IP LA
SM K3
RA G6
CA I1
CT CN
RE NN A1
HC RE D2 B
EP FC1
NS 300
M D1
EP ECP
4
CR 00 2
HU EB
AN WE BP
KR 1
D1
1
Many of these
genes are
enriched for
those involved in
dendrite
morphogenesis,
chromatin
modification and
include known
autism genes
−
0
.6
−
0
.4
−
0
.2
0
0
.2
0
.4
0
.6
0
.8
1
FGD1
TSC2
MED12
ASTN2
THRA
HUWE1
AUTS2
ATN1
ANKRD11
TSC1
DPP6
GPR37
PDLIM5
ADCY5
POGZ
FEZF2
DAGLA
HERC2
ADCY2
SMG6
SOX5
CTNND2
CREBBP
EP400
PDE1C
SATB2
RERE
YEATS2
ANK3
MED12
MAP2
SHANK1
AMPH
DLGAP2
SHANK2
LRRC7
GPR37
DPP6
PDLIM5
HCFC1
SMAD1
ADCY5
PDZD2
DLG4
GRIN2B
ADCY2
SATB2
RAI1
ZNF496
SMG6
CTNND2
SDK1
DLGAP4
CMIP
ATN1
CTTNBP2
POGZ
SLC24A2
SLC9A3
EP400
ANKRD11
SHARPIN
CBS
KIF5C
CNKSR2
CREBBP
PPP1R1B
AUTS2
MECP2
KLC2
ARID1B
SOX5
CACNA1H
TSC1
SNX19
MBD5
THRA
NSD1
CACNA1B
RPS6KA2
SBF1
BIN1
HUWE1
NRCAM
ATXN7
TSC2
EML1
APCASTN2
LPHN1
ZNF8
FGD1
CDKL5
MED12L
ZNF827
NFIA
EP300
DLGAP4
LRFN2
MTMR2
HDAC3
SYT3
PDE1C
MTM
NFIA
EP300
RERE
SYT4
CDKL5
ANK3
Nodes
LRFN2
MED12L
BZRAP1
MAP2
Chromatin Modification
NRCAM
ATXN7
DLGAP2
Dendrite Morphogenesis
Connections
YEATS2
SHANK1
AMPH
TSPOLPHN1
BIN1
Co-expression
APC
NS
Co-localization
CACNA1B
CACNA1H
Genetic Interactions
Other
Query Genes
SHANK2
RPS6KA2
MBD5
LRRC7
Non Query Genes
Pathway
SNX19
SHARPIN
SMAD1
Physical
Interactions
MECP2
KLC2
PDZD2
file
:
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r
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.
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e
b
a
r
c
h
iv
e
HCFC1
DLG4
GRIN2B
EML1
ARID1B
Predicted
KIF5C
Shared ProteinCNKSR2
Domains
P
a
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e
1
o
f1
CBS
Z
CTNND2 function?
•
Armadillo/beta-catenin superfamily, p120ctn subfamily;
•
adhesive junction associated protein that interacts
with E-cadherins;
•
interacts with presenilins;
•
transcriptional activator when bound to ZBTB33
(Kaiso) and can repress Wnt-signaling target genes;
•
Nucleocytoplasmic shuttle protein: signal?
CYFIP1: Autism gene identified in
FEMFs
Translational
Regulator
eIF4E
CYFIP1
FMRP

Variants identified in
FEMFs



Y777C (phyloP 3.54)
A1003V (phyloP
5.97)
Now shown to
simultaneously
regulate actin
polymerization
(affects spine
(De Rubeis, Neuron September 18, 2013)
morphology)
Synaptic
Signal
eIF4G
CYFIP1
eIF4E
FMRP
Thank you
<aravinda@jhmi.edu>