Using Comparative Toxicogenomics Database (CTD) to ... · PDF file Robust, publicly available...

Linda Rieswijk (PhD)GEL, University of California, Berkeley

October 31st 2017

Using Comparative Toxicogenomics

Database (CTD) to Evaluate the

Carcinogenicity of Coumarin

■ http://ctdbase.org

■ Robust, publicly available database aims to advance understandingabout how environmental exposures affect human health.

■ Release of October 2017 contains:

Chemical–gene interactions (curated) 1,621,428

Unique chemicals 12,524

Unique genes 43,714

Unique organisms 572

Gene–disease associations 21,429,161

Curated[1] 35,539

Unique genes 7,895

Unique diseases 5,526

Inferred[2] 21,393,622

Unique genes 42,727

Unique diseases 3,111

Chemical–disease associations 2,336,715

Curated[1] 208,049

Unique chemicals 9,348

Unique diseases 3,158

Inferred[2] 2,128,666

Unique chemicals 12,271

Unique diseases 5,514

1 Davis AP et al., The Comparative Toxicogenomics Database: update 2017. Nucleic Acids Res. 2016 Sep 19 [Epub ahead of print]

Comparative Toxicogenomics Database1

Workflow

■ All genes associated with chemical X (Coumarin)

■ All genes associated with disease Y (Cancer)

■ Find genes overlapped between X and Y

■ Visualize molecular/gene interaction networks

■ Look for large clusters of genes in a functionally

grouped network

■ Identify pathways in which the chemical-induced

disease genes are involved (enrichment analysis)

■ Biological pathways (~1500) can be linked with

the key characteristics of humans carcinogens

Goal: Identify Genes, Pathways & KC

Studies & Genes: Coumarin (COU) & Neoplasms (NEO)

43% (96/222) of COU_Genes overlapped with NEO_Genes

The term “neoplasms” includes curated* genes associated with cancers

of liver, lung, kidney, forestomach, pancreatic and many other types.

* Curated genes are:

1) Genes that may be a biomarker of a disease (e.g., increased expression of gene X correlates with disease Y) or play a role

in the etiology of a disease (e.g., mutations in gene X causes disease Y); or

2) A gene that is or may be a therapeutic target in the treatment of a disease (e.g., targeted reduction of gene X expression

reduces susceptibility to disease Y).

222 3152

Connectivity between Pathways using

No. of Pathways 44No. of Genes in Pathways 52No. of Genes not in Pathways 44

Affected Top 20 WikiPathways Obtained Using ClueGO(min 3 genes or 4% of total, kappa-score 0.4 and p-val<0.05)

Ten Key Characteristic Pathway Name

# of Associated

genes found

# of All associated

genes

% Associated

genesTerm

P-value

5Photodynamic therapy-induced NFE2L2 (NRF2) survival

signaling 7 24 29.17 1.271E-085 NRF2 pathway 13 146 8.90 2.925E-085 Selenium Micronutrient Network 9 89 10.11 1.637E-060 Folate Metabolism 8 67 11.94 1.813E-065 Oxidative Stress 6 31 19.35 2.109E-065 Amyotrophic lateral sclerosis (ALS) 6 38 15.79 7.364E-06

0Photodynamic therapy-induced unfolded protein

response 5 27 18.52 1.993E-058 Aryl Hydrocarbon Receptor Pathway 6 46 13.04 2.303E-055 Photodynamic therapy-induced AP-1 survival signaling 6 50 12.00 3.752E-050 Vitamin B12 Metabolism 6 52 11.54 4.710E-051 Estrogen metabolism 4 18 22.22 6.748E-051 Aflatoxin B1 metabolism 3 7 42.86 6.904E-05

11 Overview of nanoparticle effects 4 19 21.05 8.464E-051 Tamoxifen metabolism 4 21 19.05 1.282E-040 Amino Acid metabolism 7 91 7.69 1.496E-048 Aryl Hydrocarbon Receptor 5 46 10.87 2.798E-041 Metapathway biotransformation 9 179 5.03 4.326E-040 One carbon metabolism and related pathways 5 52 9.62 4.997E-041 Valproic acid pathway 3 13 23.08 5.336E-040 Trans-sulfuration and one carbon metabolism 4 31 12.90 6.114E-04

Key Characteristics of Coumarin-Associated Pathways (n=44 from 52 involved genes)

Ten Key Characteristics # Associated Pathways

1. Metabolic activation 8

2. Genotoxicity 0

3. Altered DNA repair 1

4. Epigenetic alterations 0

5. Oxidative stress 10

6. Chronic inflammation 3

7. Immunosuppression 0

8. Modulation of receptor 3

9. Immortalization 0

10. Altered cell proliferation 3

Not Applicable (0) 14

Multiple characteristics (11) 2

Oxidative Stress

More oxidative stress (KC5) and metabolic activation (KC1) pathways are affected;

Five key characteristics are involved in the potential carcinogenicity of coumarin.

Summary of Coumarin-involvedGenes, Pathways & Key Characteristics

Summary # Genes/Pathways/KCs

CTD: Coumarin Genes 222

CTD: Neoplasm Genes 3152

CTD: Overlap COU-Genes and NEO-Genes 96

ClueGO: # of Genes not present in Pathways 44

ClueGO: # of Genes present in Pathways 52

ClueGO: Number of Pathways 44

wikiPathway: # of Key Characteristics involved 5 of 10

Luoping ZhangGEL, University of California, Berkeley

November 2, 2017

Thank You !