1. Anders Dohlman BD2K-LINCS DCIC Ma’ayan Lab 11/29/16
Predicting Adverse Cardiovascular Events for Tyrosine Kinase Inhibitors from Molecular Features
Anders Dohlman
BD2K-LINCS DCIC
Ma’ayan Lab
11/29/16

2. Cardiac Effects of TK Inhibition
Hypertension high blood pressure Hypertrophy thickened ventricular septum Cardiomyopathy decrease in contractility Ejection fraction decrease less blood leaving heart Pulmonary odema buildup of fluid in the lung

3. ACEs Bit Matrix + FAERS FDA Drug Labels
EBGM score: how much more likely a drug-event pair are to occur together versus the two occurring independently
a two sided 90% confidence interval is given, we used an EB05 score of 2 or greater to consider an association
ie. “we are 95% sure than is adverse event occurs at least twice as often with the drug than they do independently”
FDA Drug Labels

4. ELISA –– Kinase Inhibition
No ACE
Decreased Ejection Fraction
Cardiac Failure
Hypertension
ELISA = enzyme immunoassay
Measures kinase affinities for small molecules relative to an immobilized ligand
Reports as % inhibition of kinase relative to immobilized ligand
Data from Uitdehaag et al. (PLoS ONE, 2014)

5. Random Forest Classification Scheme
Reported
F1 score is essentially an average of precision & sensitivity
precision =  # true positives / # test outcome positives
sensitivity = # true positives / # condition positive
Not
Reported
INPUT
TKI signatures
Molecular features
OUTPUT
ACE Predictions
Feature importance

6. ELISA Canvas Analysis Any Cardiac Failure Decreased EF Hypertension
Least important
Most important
Tiles are arranged to place co-inhibited kinases adjacently. Each canvas is a torus.
Any
Cardiac Failure
Decreased EF
Hypertension
PDGFRA
PDGFRA_V561D
FLT4
KIT
EGFR
ABL_E255K
ABL
ARG
CDK4/CycD3
LKB1
CDK9/CycT1
CDK3/CycE1
KDR
KIT_T670I
FLT1
FLT4
RET_M918T

7. Hypertension is predicted by VEGFRs, cKIT, RET
ADR
no ADR
Hypertension is predicted by VEGFRs, cKIT, RET
FLT1 and KDR form a heterodimer
PI3K/AKT promotes neural growth
PI3K/AKT pathway is involved in Long-term Potentiation (PI3K necessary & sufficient for LTP)
% Inhibition
FLT1 (VEGFR1)
KDR (VEGFR2)
KIT –– proto-oncogene implicated in GIST, AML
RET –– cadherin family, involved in neuronal navigation
/ promote angiogenesis & vascular development

8. Cardiac Failure is predicted by ABLs, cKIT, PDGFR
ADR
no ADR
Cardiac Failure is predicted by ABLs, cKIT, PDGFR
EGFR regulates PI3-K-Akt Signaling, STAT, Ras-Raf-Mek-Erk pathways
% Inhibition
ABL (ABL1)
ARG (ABL2)
KIT –– proto-oncogene implicated in GIST, AML
PDGFRA –– organ development, wound healing, proliferation
/ NRTKs, regulate cytoskeleton remodeling, motility

9. LINCS Transcripomics –– L1000
Based on FLEXMAP 3D System by Luminex
Measures 1000 “landmark” genes per experiment, and uses these to infer expression of the full transcriptome
Minimally redundant
Widely expressed across cellular contexts
Over 1.5 million gene expression profiles in total
20,413 chemical compounds
22,119 genetic perturbations
77 cell lines profiled
80%

10. LINCS Transcripomics –– DToxS
Seeks to obtain cellular signatures related to adverse effects caused by FDA-approved drugs
Four adult PromoCell cardiomyocyte cell lines
38 drugs
570 transcriptional experiments
114 proteomic experiments

11. Trace of Performance
L1000 F1
DToxS F1
Genes

12. Trace of Performance
L1000 F1
~50
DToxS F1
~12
Genes

13. Pathway Analysis Using Gene Set Enrichment
ACEs M f
Kinase Inhibitors
Gene Expression
Enrichment Features

14. Pathway Analysis Using Gene Set Enrichment
500 down
500 up
Gene Signature
ACEs M f
Kinase Inhibitors
Gene Expression
Enrichment Features

15. Pathway Analysis Using Gene Set Enrichment
500 down
500 up
Gene Signature
ACEs M f
Kinase Inhibitors
Gene Expression
Enrichment Features

16. Pathway Analysis Using Gene Set Enrichment
500 down
500 up
Gene Signature
Enrichment Vector
ACEs M f
Kinase Inhibitors
Gene Expression
Enrichment Features

17. Pathway Analysis Using Gene Set Enrichment
Hypertension
Cardiac Failure
Decreased Ejection Fraction
Indeed, a study of Imatinib suggests that calcium-induced loss of mitochrochondrial membrane potential and a reduction of cellular ATP leads to cell death
Gini

18. Pathway Analysis Using Gene Set Enrichment
Hypertension
Cardiac Failure
Decreased Ejection Fraction
Indeed, a study of Imatinib suggests that calcium-induced loss of mitochrochondrial membrane potential and a reduction of cellular ATP leads to cell death
Significant enrichment for transmembrane ion channels, particularly Ca2+
...these channels play a fundamental role in neuromuscular signaling, muscle contraction

19. Conclusions
Screening ELISA binding data to identify kinases predictive of adverse cardiac events
Cardiac Failure: ABL1, ABL2
Decreased Ejection Fraction: cyclin-kinase complexes
Hypertension: VEGFRs, c-Kit
Binding of drug-resistant c-Kit mutants are stronger predictors of hypertension than the c-Kit wild-type
ATP-binding site: V654A, T670I
Screening of LINCS L1000, DToxS data for genetic biomarkers of adverse cardiac events
Peak performance with 12 or 50 genes, respectively
Enrichment analysis of predictive genes reveals potential mechanisms of hypertension & cardiac dysfunction
Ca2+-induced mitochondrial membrane potential collapse
Potentially due to deregulation of PKA in cardiomyocytes
F1 score is essentially an average of precision & sensitivity
precision =  # true positives / # test outcome positives
sensitivity = # true positives / # condition positive

20. Acknowledgements
Avi Ma’ayan Darrell Abernethy Shadia Zaman ... Qiaonan Duan Simon Koplev Zichen Wang The Ma’ayan Lab
F1 score is essentially an average of precision & sensitivity
precision =  # true positives / # test outcome positives
sensitivity = # true positives / # condition positive