Mechanistic models of CMap

drug perturbation
functional profiles
María Peña-Chilet, PhD
Clinical Bioinformatics Area - FPS/CIBERER, Seville, Spain
14th July, Annual International Conference on
Critical Assessment of Massive Data Analysis (CAMDA)
Big Omics Era

Improvement of sequencing and

molecular biology technologies.

Huge amount of transcriptomic

data generation.

Repositories and public databases

Generation of data driven

knowledge.

1
It’s all about the (cellular) context

CELLULAR CONTEXT
- Transcriptome data
analyses.
PATHWAY
- Gene expression
analysis.

FUNCTION
MECHANISTIC
INTERACTOME
- Assess cellular EPIGENETICS
function. GENE

- Enrichment analysis.

2
It’s all about the (cellular) context

CELLULAR CONTEXT
- Transcriptome data
analyses.
PATHWAY
- Gene expression
analysis.

FUNCTION
MECHANISTIC
INTERACTOME
- Assess cellular EPIGENETICS
function. GENE

- Enrichment analysis.

2
It’s all about the (cellular) context

CELLULAR CONTEXT
- Transcriptome data
analyses.
PATHWAY
- Gene expression
analysis.

FUNCTION
MECHANISTIC
INTERACTOME
- Assess cellular EPIGENETICS
function. GENE

- Enrichment analysis.

2
It’s all about the (cellular) context

CELLULAR CONTEXT
- Transcriptome data
analyses.
PATHWAY
- Gene expression
analysis.

FUNCTION
MECHANISTIC
INTERACTOME
- Assess cellular EPIGENETICS
function. GENE

- Enrichment analysis.

2
It’s all about the (cellular) context

CELLULAR CONTEXT
- Transcriptome data
analyses.
PATHWAY
- Gene expression
analysis.

FUNCTION
MECHANISTIC
INTERACTOME
- Assess cellular EPIGENETICS
function. GENE

- Enrichment analysis.

2
It’s all about the (cellular) context

CELLULAR CONTEXT
- Transcriptome data
analyses.
PATHWAY
- Gene expression
analysis.

FUNCTION
MECHANISTIC
INTERACTOME
- Assess cellular EPIGENETICS
function. GENE

- Enrichment analysis.

2
Mechanistic Pathway Analysis
FUNCTIONAL PATHWAY
ANALYSIS METHODS

3
A. Amadoz, et al. 2018. A comparison of mechanistic signaling pathway activity analysis methods. Briefings in Bioinformatics
Mechanistic Pathway Analysis
FUNCTIONAL PATHWAY F1
ANALYSIS METHODS
Gene set enrichment analysis (GSEA)

F2

GSEA

3
A. Amadoz, et al. 2018. A comparison of mechanistic signaling pathway activity analysis methods. Briefings in Bioinformatics
Mechanistic Pathway Analysis
FUNCTIONAL PATHWAY F1 F1
ANALYSIS METHODS
Gene set enrichment analysis (GSEA)

Pathway topology based (PT-based):

Analyzes the connection between genes
F2 F2
based in the topology of the interactions.

GSEA PT-based

3
A. Amadoz, et al. 2018. A comparison of mechanistic signaling pathway activity analysis methods. Briefings in Bioinformatics
Mechanistic Pathway Analysis
FUNCTIONAL PATHWAY F1 F1
ANALYSIS METHODS
Gene set enrichment analysis (GSEA)

Pathway topology based (PT-based):

Analyzes the connection between genes
F2 F2
based in the topology of the interactions.

Mechanistic Pathway Analysis (MPA):

Analysis of the functional activation
according to topology and type of
interaction between genes within a GSEA PT-based MPA
given signalling network.

3
A. Amadoz, et al. 2018. A comparison of mechanistic signaling pathway activity analysis methods. Briefings in Bioinformatics
Hipathia

Gene interactions directed SIGNALING PATHWAYS

network.

Based in biological evidence. HIPATHIA

Allows integration of tissue gene

expression data. FUNCTIONAL
ANNOTATION

Provides cell functional context.

Mechanistic model.
4
Hipathia

- Gene expression.

- Protein interactions: ACTIVATION/INHIBITION

- Signal propagation that simulates cell signal

transduction.
RECEPTOR EFFECTOR
- Differential functional activity profiles.
Hidalgo MR, et al. 2016. High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant 5
clinical outcomes. Oncotarget.
Hipathia

6
Hipathia

MPA methods comparison

Hipathia

65% accuracy predicting therapeutic targets in

several cancer cell lines. 7
Drug development and drug repurposing

Less than 12%

make it to
clinical trials

YEARS
12 years to approve a drug 8
Connectivity Map
NIH Fund program.

Catalogs human cells response to

perturbations.

A set of resources including

databases, computational methods
and tools.

Integrated picture to understand

human disease and therapy
development.
A. Subramanyan, R. Narayan, S.M. Corsello, et al., A next generation connectivity map: L1000 platform and the first 1,000,000 profiles, 9
Cell 171 (6) (2017)1437–1452,https://doi.org/10.1016/j.cell.2017.10.049.
LINCS L1000

LINCS: The Library of Integrated Network-Based Cellular Signatures

L1000: Gene expression

Affymetrix panel of 1000
genes.

Imputation of the expression

of all the genes. 10
Searching for the opposite effect

- Effect of drugs and compounds over

gene expression.

- Gene expression profile:

DISEASE vs DRUG
- Search for opposite profiles to
compensate the effect that a disease
has in gene expression.
- Mechanistic approach.

11
Searching for the opposite effect
- Compare data from cell lines and data
from patient?
- Data from BRCA patients from TCGA.

- Data from BRCA cell lines from CLLE.

- ML train with patients data a

mechanistic model to evaluate the
response to in silico perturbations.
- Similar performance patients data
predicted vs Cell line data predicted.

I. Álamo, C. Loucera, M. Peña-Chilet, J. Dopazo, Machine learning model for predicting perturbation functional impact from 12
breast cancer cell lines to patients, 2020. Unpublished data.
Methodology: Data

Data available: Data used:

19,811 molecules 5,795 molecules

70 cell lines 30 cell lines

473,647 gene 38,824 activity

signatures signatures

Gene Expression Omnibus: The Cancer Genome Atlas (TCGA):

Dataset diabetes: GSE25724 23 cancer tissue
Paired normal tissue
13
Methodology: Workflow
Functional pathway
5796 molecules activation paired
DRUG PROFILE

Gene analysis Fold Change

Treated: 24h at 10mM expression Treated Drug1 2 … n
Function 1 DRUG
profile vs 2
30 cancer cell lines Untreated …
n
+
Control cell lines HIPATHIA CO
LIMMA RR
EL
AT
IO
N
DISEASE PROFILE

TCGA: Tumour tissue Fold Change

+ Drug1 2 … n
Normal tissue Cases Function 1
Gene vs 2
Controls …
Pancreatic tissue with expression n DISEASE
profile Functional pathway
diabetes activation differential
analysis 14
Results
Cell lines used from 14 different
tissues.

Data structure:
gene expression data used vs
pathway activity.
PCA: Gene expression 15
Results
Cell lines used from 14 different
tissues.

Data structure:
gene expression data used vs
pathway activity.
PCA: Pathway activity 15
Results

Effect of 5,796
compounds

Activity of 1098 circuits

from 79 physiological
pathways.

988 compounds with at

least one significant
circuit.

16
Results

p-value < 10-4 17

Results

p-value < 10-4 17

Results

p-value < 10-4 17

Results

p-value < 10-4 17

Results

Correlation between drugs and diseases.

Highlight some interesting findings.

18
Results

18
Next steps

Predict the pathway activities using ML from L1000 genes instead of using
imputed data.
Analyze cell expression data as temporal series.
Search for combinations of molecules that revert disease profile.
Use GTEx gene expression data as a template to infer drug effect in different
tissues.
Model the extrapolation of the drug functional effect from cell line to actual
patient tissue.
Account for genomic variability when available.
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Applications

Evaluate the functional profile of a new molecule.

Design new molecules for pathway-targeted therapy.

Function-driven new drugs screening.

Search for drug profiles opposite to patient profile. Personalized

medicine.

Efficient drug repurposing in silico testing.

20
THANK YOU!
Marina Esteban

Macarena López
IMPUTATION METHOD CMAP - LINCS

From the original Affymetrix Connectivity Map assay, They selected a

number genes ranging from 100-10,000, and they generated with these
an imputed version of the affymetrix using (OLS) Ordinary least squares
regression with the genes, the landmarks, as the independent
variables, and assessed the percentage of connections that were
recovered.
They used a method similar to that described in a Nature Methods
article, Donner 2012, if you want to check.