Predicting Adverse Cardiovascular Events for Inhibitors from Molecular Features

Anders Dohlman BD2K-LINCS DCIC Ma’ayan Lab 11/29/16 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 ACEs Bit Matrix

FAERS

+

FDA Drug Labels ELISA –– Kinase Inhibition No ACE

Cardiac Failure Decreased Ejection Fraction Hypertension

Data from Uitdehaag et al. (PLoS ONE, 2014) Random Forest Classification Scheme

Reported

Not Reported

INPUT OUTPUT – TKI signatures – ACE Predictions – Molecular features – Feature importance ELISA Canvas Analysis Least important Most important Tiles are arranged to place co-inhibited kinases adjacently. Each canvas is a torus. Any Cardiac Failure Decreased EF Hypertension

1. PDGFRA 1. ABL_E255K 1. CDK4/CycD3 1. KDR 2. PDGFRA_V561D 2. ABL 2. LKB1 2. KIT_T670I 3. FLT4 3. ARG 3. CDK9/CycT1 3. FLT1 4. KIT 4. CDK3/CycE1 4. FLT4 5. EGFR 5. RET_M918T ADR no ADR

Hypertension is predicted by VEGFRs, cKIT, RET

% Inhibition

FLT1 (VEGFR1) / promote angiogenesis & vascular development KDR (VEGFR2)

KIT –– proto-oncogene implicated in GIST, AML

RET –– cadherin family, involved in neuronal navigation ADR no ADR

Cardiac Failure is predicted by ABLs, cKIT, PDGFR

% Inhibition

ABL (ABL1) ARG (ABL2) / NRTKs, regulate cytoskeleton remodeling, motility

KIT –– proto-oncogene implicated in GIST, AML

PDGFRA –– organ development, wound healing, proliferation LINCS Transcripomics –– L1000

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

F1 L1000

DToxS F1

Genes Trace of Performance

F1 L1000

~50

DToxS F1

~12 Genes Pathway Analysis Using Gene Set Enrichment

ACEs

M f Kinase Inhibitors

Gene Expression Enrichment Features Pathway Analysis Using Gene Set Enrichment

500 down 500 up Gene Signature

ACEs

M f Kinase Inhibitors

Gene Expression Enrichment Features Pathway Analysis Using Gene Set Enrichment

500 down 500 up Gene Signature

ACEs

M f Kinase Inhibitors

Gene Expression Enrichment Features Pathway Analysis Using Gene Set Enrichment

500 down 500 up Gene Signature

Enrichment Vector

ACEs

M f Kinase Inhibitors

Gene Expression Enrichment Features Pathway Analysis Using Gene Set Enrichment

Hypertension Cardiac Failure Decreased Ejection Fraction

Gini Pathway Analysis Using Gene Set Enrichment

Hypertension Cardiac Failure Decreased Ejection Fraction

Significant enrichment for transmembrane ion channels, particularly Ca2+ ...these channels play a fundamental role in neuromuscular signaling, muscle contraction Conclusions

I. 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

II. Binding of drug-resistant c-Kit mutants are stronger predictors of hypertension than the c-Kit wild-type – ATP-: V654A, T670I

III. Screening of LINCS L1000, DToxS data for genetic biomarkers of adverse cardiac events – Peak performance with 12 or 50 genes, respectively

IV. 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 Acknowledgements

Avi Ma’ayan Darrell Abernethy Shadia Zaman ... Qiaonan Duan Simon Koplev Zichen Wang ... The Ma’ayan Lab