A Pan-Cancer Signature Catalog
to Classify Tumor Mixtures:
Application to Recognition of
Metastatic Disease in Prostate Cancer
Kiley Graim
UC Santa Cruz
Motivation
TCGA has many high quality
primary tumor samples,
but metastasis kills
Which primaries will metastasize?
Image courtesy of wikimedia commons
1
3 Possible Scenarios
Primary Subtype
Metastatic Subtype
?
?
?
?
Do a restricted subset of primary subtypes share gene
expression signatures with metastatic disease?
If true, may use signature as an early sign of aggressive disease.
2
Multiple Datasets to Define Primary and
Metastatic Gene Expression Signatures
• n
Dataset # Normal # Primary
Cai (2011)
Chandran (2007)
Grasso (2012)
GTEx (2014)
Monzon (2007)
Taylor (2010)
TCGA
Joint
0
0
28
42
52
29
21
172
22
10
59
0
65
131
246
533
# Metastatic
29
21
32
0
25
19
0
126
831 Samples (659 Tumor)
# Genes
10,523
14,997
15,830
13,256
9,383
19,923
20,500
4,895
3
Removal of Batch and Dataset Effects
• << newBefore
before/after combat PCA plots
After>>
• << add indicat
Batch effect removal via COMBAT (R package ‘sva’)
4
Removal of Batch and Dataset Effects
• << newBefore
before/after combat PCA plots
After>>
• << add indicat
Batch effect removal via COMBAT (R package ‘sva’)
5
K=4
4 Primary Subtypes
Identified from
Multiple Datasets
(Including TCGA)
6
Primary Subtype Predictors
• Multinomial elastic
net to predict
primary subtypes
• Trained using
primary data
• Leave-one-out
cross-validation
• Apply to metastatic
samples
Samples
Subtype 1 vs. Not
Subtype 2 vs. Not
Subtype 3 vs. Not
Subtype 4 vs. Not
Not Subtype
Subtype
7
How Robust Are the Predictors?
True
Predicted
cluster
1
2
3
4
4
0
0
0
1
3
0.010
0
0.990
0
2
0.017 0.983
0
0
1
0.990 0.010
0
0
Balanced Success Rate = 0.991
8
K=3
3 Met Subtypes
Identified from
Multiple Datasets
(None TCGA)
9
The Majority of Mets
Are Predicted to Be Primary Subtype 2
Met-like
primaries
Predicted Primary Cluster
10
Met-Like Primaries Have Higher Gleason
and Higher Tumor Grade
Met-like
primaries
pval = 0.0e-3
FDR = 0.0e-3
pval = 0.0e-3
FDR = 0.0e-3
11
Predisposition for
Movement and Metastasis
MILI_PSEUDOPODIA_HAPTOTAXIS_UP
BIDUS_METASTASIS_UP
pval = 0.0e-3
pval = 0.0e-3
FDR = 0.0e-3
FDR = 0.0e-3
12
Are There Networks that Distinguish
Differential pathway activity analysis
Met-like Primaries from the Others?
Activity up in Group A
(relative to group B)
Activity down in Group
A (relative to Group B)
Pathway Activities
Pathway Activities
Pathway
Signature
high activity
low activity
13
Josh Stuart Group
PathMark Overview of
Distinguishing Networks of
Met-Like Primaries
14
Proliferation-Related
Subnetwork
15
MYB/MYC
Subnetwork
16
Acknowledgements
 Yulia Newton
 Adrian Bivol
 Robert Baertsch
 Artem Sokolov
 Christina Yau (Buck Institute)
 Joshua M. Stuart
17
18
TCGA
Taylor
Joint primaries,
mets, normals
Exponential
Normalization
Combat
Normalized
joint
Batch effect
adjusted joint
…
Primaries
Subtype
Pipeline
Mets
Consensus
Clustering
19
20
21