genetics variations effects, propagation, and buffering · 2016-04-27 · genetics variations –...
TRANSCRIPT
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Teresa Przytycka
NIH / NLM / NCBI
Genetics variations –
effects, propagation, and
buffering
AlgoCSBAlgorithmic Methods in Computational and Systems Biology
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Journal “Wisla” (1902)
Phenotypes
Genotypes Individuals 1 2 3
gen
om
e 1
gen
om
e 2
gen
om
e 3
genetic
variations
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Molecular
Phenotypes
Genotypes Gene Expression of gene g
Individuals 1 2 3 Individuals 1 2 3
gen
om
e 1
gen
om
e 2
gen
om
e 3
eQTL analysis
genetic
variations
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Molecular
Phenotypes
Genotypes Gene Expression of gene g
Individuals 1 2 3 Individuals 1 2 3
No one-to-one relation in most cases
• Pathways rather than individual genes
• Drivers versus passengers
• Role of context and stochastic variations
gen
om
e 1
gen
om
e 2
gen
om
e 3
genetic
variations
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Lessons from
engineered genetic perturbations
in Fly
5
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Engineered chromosomal deletions
6
Left arm of chromosome 2
Chromosomal deletions (in one chromosome only)
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Engineered chromosomal deletions
7
Left arm of chromosome 2
Chromosomal deletions (in one chromosome only)
Expression of deficiency genes is reduced by nearly half
(but not exactly and not always)
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What is the impact on network neighbors?
1st order neighbors 2nd order neighbors 3rd order neighbors
deficiency gene
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9
Expression changes propagate through the
network up to the second order neighbors
First order neighbors
Second order neighbors
Third order neighbors
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Expression variation of deficiency genes is
higher than other genes
10
Measurement of variability
Delta = abs(e1-e2) /ave(e1,e2)
e1,e2 – expression in experiment 1 and 2
exp
ressio
n v
aria
bili
ty
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Expression bursts as major contributor to
single cell expression noise
11
Prediction from the model – increased copy copy number reduces
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Single cell model does not explain
variability in expression of deficiency genes
12
Technical noise
exp
ressio
n v
aria
bili
ty
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-4 -3 -2 -1 0 1
0.0
0.5
1.0
1.5
Female
log2 Fold Change (Df/+ vs. Control)
De
lta
-3 -2 -1 0 1
0.0
0.5
1.0
1.5
Male
log2 Fold Change (Df/+ vs. Control)
De
lta
Deficiency genes with
compensated/collapsed expression are
more noisy
compensated
collapsed
½ of wild-type expression
(expected)
exp
ressio
n v
aria
bili
ty
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14
-4 -3 -2 -1 0 1
0.0
0.5
1.0
1.5
Female
log2 Fold Change (Df/+ vs. Control)
De
lta
-3 -2 -1 0 1
0.0
0.5
1.0
1.5
Male
log2 Fold Change (Df/+ vs. Control)
De
lta
Deficiency genes with
compensated/collapsed expression are
more noisy
compensated
collapsed
½ of wild-type expression
(expected)
exp
ressio
n v
aria
bili
ty
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15
-4 -3 -2 -1 0 1
0.0
0.5
1.0
1.5
Female
log2 Fold Change (Df/+ vs. Control)
De
lta
-3 -2 -1 0 1
0.0
0.5
1.0
1.5
Male
log2 Fold Change (Df/+ vs. Control)
De
lta
Deficiency genes with
compensated/collapsed expression are
more noisy
compensated
collapsed
½ of wild-type expression
(expected)
exp
ressio
n v
aria
bili
ty Hypothesis:
dosage compensation
and expression noise
are related to
interaction context
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Expression variations propagate across
regulatory network
16
TFNon-TF
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Why this is relevant
17
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Copy number variations and
propagation of expression
changes in cancer
18
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Positive correlation between gene copy
number and gene expression in cancer (GBM)
19
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Molecular Phenotypes Genotypes (gene expression)
Individuals 1 2 3 4
gen
om
e 1
gen
om
e 2
gen
om
e 3
gen
om
e 4
CNV
Using propagation of expression perturbation to
study genotype-phenotype relation
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The eQTL-net method
expression of
gene of interest
eQTL relation
Motivated in part by:
Tu et al Bioinformatics 2006
Suthram et al MSB 2008
Kim et al. PLoS CB 2011
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Explaining eQTL associations by propagation
of expression changes
eQTL relation
gene of interest
genes in CNV region
Kim et al. PLoS CB 2011
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Explaining eQTL associations by propagation
of expression changes
Kim et al. PLoS CB 2011
gene of interest
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Identification of information propagation
pathways and driver genes
driving gene
Kim et al. PolS CB 2011
gene of interest
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How to interpret these pathway in the context
of throughput interaction networks?
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Dutch Interior 1, Joan Miro’ (1893–1983) Museum of Modern Art, New York© 2012 Successió Miró / Artists Rights Society (ARS), New York / ADAGP, Paris used with ARS permission).
How to interpret this painting?
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REAL NETWORK
Dutch Interior 1, Joan Miro’ (1893–1983)
Museum of Modern Art, New York© 2012 Successió Miró / Artists Rights Society (ARS), New York / ADAGP, Paris
(used with ARS permission).
The Lute Player, Hendrick Maertensz Sorgh (1610-1670),
Rijksmuseum, Amsterdam(public domain)
Details are perturbed but relationships remain
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eQTL relation
gene of interest
Considering information propagation
pathway as a bag of genes
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Typically we use many genes as a molecular
phenotype- repate the process for all of them
eQTL relation
eQTL relation
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Results
30
Driving Copy Number alterations
EGFR, PTEN, RB1, GBAS, TP53, CDKN2A,…..
Reoccurring pathways
Cell cycle, EGFR, RAS, Cell proliferation, Insulin Signaling, DNA repair, ….
Splicing, SMAD (nuclear translocation), lipid storage
Hubs
Myc, E2F1, CREBBP, SP1, Jun,…
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Utilizing Networks for Understanding
Genotype-Phenotype relations
Network
propagation
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What can we do about perturbations that do not
necessarily cause expression change in network
neighbors?
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mutated /
dysregualted
subnetworks
d networks
Finding mutated/dysregulated
subnetworks
If different perturbations have similar effects the
perturbations should be related – belong to the
same subnetwork
Main principle:
Challenge:
Cancer heterogeneity
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Gene cover
Module Cover Approach
Find minimal cost set of
modules so that each
disease case is covered at
least k times
Optimization problem:
Cost is a determined by:
A similarity of genes within modules
(application dependent)
number of modules
Kim et al. 2013
a
Advantage: different patients can be covered by different subnetworks
Motivated in part by: Ulitsky et al 2008
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Gene cover
Optimization problem:
Cost is a function of:
Similarity within modules
• Distance in network
• Expression similarity
(similarity of eQTL profiles)
number of modules
(parameterized penalty)
Kim et al. 2013
Application 1: Glioblastoma Analysis
Advantage: different patients can be covered by different subnetowrks
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Modules capture patients heterogeneity/subtypes
cases
mo
du
les
Kim et al. PSB 2013
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Application 2: Extension to mutual
exlusivity
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Mutual exclusivity of cancer drivers
mutations in gene 1
Mutations in gene 2
patients
Thomas et al 2007
Ciriello, et al., 2012;
Vandin, et al., 2012;
Szczuret et.al , 2014, 2015
Leiserson, et al., Vadin et al. 2013,2014,2015;
Kim et al. 2015
Constantinescu et al. 2015
Proposed explanations
• any of the two drivers alone gives sufficient growth advantage
• negative genetic interactions between drivers
Interesting property
Mutual exclusive pairs are often in the same pathway
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Application 2: Subnetworks dysregulated
across many cancer types
39
Gene cover
Cost is a function of:
Similarity measure
• Distance in network
• Mutual Exclusivity Score
number of (parameterized
penalty)
Kim et al. 2015
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Defining Mutual exclusivity in PanCancer
setting
mutations in gene 1
Mutations in gene 2
patients
patients
gene 1
gene 2
Kim et al. IMSB 2015 – classification of ME types in context of PanCancer and properties of
different ME types
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MEMCover (Mutual Exlusivity Module Cover)
Finds subnetwokrs dysregulated across cancer types
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Kim et al. IMSB 2015
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Kim et al. IMSB 2015
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MEMCover modules are enriched in cancer
drivers?
44
Compared to Module Cover without ME Compared to HotNet2
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mutated /
dysregualted
subnetworks
d networks
Utilizing Networks for Understanding
Genotype-Phenotype relations
Perturbation
flow
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mutated /
dysregualted
subnetworks
d networks
Patient/phenotypic similarity networks
phenotypic
similarity
networks
Perturbation
flow
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Motivation – simultaneous utilization of
multiple genotypic/causal and phenotypic
data types
47
Genotypic/ causal factors
mutations,
CNV
methylation,
Sex, age, environment ….
Phenotypic properties
gene expression
response to drugs
survival time
pathology features
Idea: Construct phenotype similarity graph and
explain it connectivity using genotypic features
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Topic model: Assuming that each document is a
mixture of topics - identify topics and the words that
define them
Chang J, Blei DM: Hierarchical Relational Models for Document Networks. Ann Appl
Stat 2010, 4(1):124-150.
Document similarity network
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Subtype I
EGFR_A 0.45
NF1_M 0.37
PTEN_A 0.21
….
Subtype II
PDGFA_A 0.51
IDH1_M 0.29
M53_M 0.17
….
Subtype III
mirR218_H 0.38
ICDK2_D 0.22
SHC1_M 0.14
….
Subtype IV
CDK2B_D 0.37
EGFR_A 0.25
….
Features:EGFR_A
NF1_M
CDKN2B_D
.
.
;
Topics – disease subtypes
Words – possible causes (mutations, CNV, miRNA)
Documents similarity– phenotypic similarity (gene expression)
Cho et al. NAR 2013/RECOMB 2012
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Cho et al. NAR 2013/RECOMB 2012
Similar patients are to be explained by similar
subtypes mixtures
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Co-occurrence of patients in the same
subtype (based on 1000 topic models)
Observation: No separate Neural group
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Loss of Neural group is not surprising
52
expression similarity network for GMB
Mesenchymal
Classical
Proneural
Neural
Varhaak et al.
Classification
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Mesenchymal
EGFR_A
NF1_M
NF1_A
PTEN_A
BRACA2
BRACA1
….
Preneural
PDGFA_A
IDH1_M
Mir 128a/b
Mir 124a….
ErBB1/2
Subtype IIIClassical
TNFRSF
….
(no clearly
dominating one)
Features:EGFR_A
NF1_M
CDKN2B_D
.
.
;
Subtypes are defined by a distribution of words
(mutations) – new patients can be easily
classified
Cho et al. NAR 2013/RECOMB 2012
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mutated /
dysregualted
subnetworks
d networks
Summary – these are complementing
approaches
phenotypic
similarity
networks
Perturbation
flow
eQTL-net
Module-Cover Topic Model
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Przytycka’s group
Phung Dao Jan Hoinka YooAh Kim Damian Wojtowicz Yijie Wang
AlgoCSBAlgorithmic Methods in Computational and Systems Biology
DongYeon Cho Sanna Madam
(alumnae) Poolesville HS
Collaborators
Brian Oliver Hangnoh Lee
Steve Russel, Cambridge
Stefan Wuchty, Univ. Miami (not pictured)
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56
Perturbing a systems brings about valuable lessons