An introduction11

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An introduction

Connectivity Map: the use for drug-repurposing

Speaker Wu-Lung Roger Yang 楊伍隆

Advisors Prof. Chi-Ying Huang ⿈黃奇英

Prof. Kun-Mao Chao 趙坤茂

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Central Dogma

•DNA

•RNA•Protein

•DNA

•RNA•Protein

DNA $$

RNA$

Protein$

transcription

translation

duplication

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Extended central dogma

copy number variation SNP

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Technology available

DNA

Sequencing, Next generation sequencing (NGS)

SNP array RNA

microarray NGS

Protein

protein array

mass spectrometry

DNA $$

RNA$

Protein$

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References

Science 313(5795): 1929-1935.

Nature Reviews Cancer 7(1): 54-60.

Cited in Scopus: 750 (as May 4, 2013)

Cited in Scopus: 137 (as May 4, 2013)

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Goals

Create a large drug- response profile

database.

Use microarray profiles

to query best matching

or mismatching drugs

Drug repurposing

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http://2.bp.blogspot.com/_cwleTqQx7ks/TIkHQJSm-uI/AAAAAAAAABU/feudFmSg4MY/s1600/DNA+microarray.jpg

Microarray

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Goals

Control Treatmen t

Cell Cell + Drug

Gene Control Treatme nt Fold Change

A 1 5 5/1

B 1 1 1/1

C 5 1 1/5

...

measurement of

mRNA

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Drug 1 Drug 2 Drug 3 Drug ... Drug N

Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Gene 6 Gene ...

Gene M

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Drug Similarity

Compare

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Drug Repurposing

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http://www.msd.com.hk/health_info/drug_education/e_ddp_introduction.html

Drug Development Process

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Ashburn, Ted T, and Karl B Thor. 2004. “Drug repositioning: identifying and developing new uses for existing drugs.” Nature Reviews Drug Discovery

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Nature Reviews Drug Discovery 12, 87-90 (February 2013) | doi:10.1038/nrd3946

2007: 69 drugs, but 16 are new drugs

average 15 years and US$800 million for a new drug to market

New drugs approved by FDA each year remain at 20~30 compounds.

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New uses for old drugs

Nobel laureate James Black

Nature 448, 645-646 (2007)

"The most fruitful basis for the discovery of a new drug is to start with an old drug"

Chong, Curtis R, and David J Sullivan. 2007. “New uses for old drugs.” Nature 448(7154): 645–646.

New uses for old drugs

“The most fruitful basis for the discovery of a new drug is to start with an old drug”

-- Nobel laureate James Black

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Drug repurposing examples

Viagra for erectile dysfunction Nelfinavir for cancer

Tamoxifen for bipolar disorder

Gleevec for rheumatoid arthiritis

Pentylenetetrazole for Down Syndrome Astemizole for malaria

Lipitor for alzhemimers

Lipitor for influenza mortality Metformin for cancer

CDD Community Group Meeting, SFO, Oct 1, 2009

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Database

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Drugs

1309 small molecules

680 drugs have

been conducted 4 times each.

6100 instances

7056 microarrays

0 175

350 525 700

49 43

162

680

226

87 13 17 3

1 2 3 4 5 6 7 8 9 Num of Instances

Drug Co unt

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Drug dosage

Most drugs are tested between 1µM and 20µM

Co un t

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Dose count

0 375 750 1125 1500

Number of doses

6 5 4 3 2 1

1225

10 72 1

0 1

Instance Count v.s. Number of Doses

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Duration

Most drugs are conducted for 6 hours.

Primary effects, not second effects

0 1750 3500 5250 7000

6 Hours 12 Hours

4 6096

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Cell Type

0 1000 2000 3000 4000

MCF7 PC3 HL60 ssMCF7 SKMEL5

17 18

1229 1741

3095

MCF7 Breast cancer PC3 Prostate Cancer

HL60 Leukemia

ssMCF7 Breast cancer

charcoal-stripped serum

SKMEL5 Skin Cancer

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Fold Change

64% of 6100 instances have less than 2% of probes having 2-Fold change.

Percentage of probes with 2-Fold change

0 750 1500 2250 3000

<1%

1%~2%

2%~3%

3%~4%

4%~5%

5%~6%

6%~7%

7%~8%

8%~9%

>10%

128 197 80 70

219 132 381

1005 1967 2021

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Instances

Each instance is defined as one drug treatment over a sample of controls.

e.g. cells treated with vorinostat versus untreated ones.

Instance = Drug type x Cell type x Duration x Dose

e.g. 10µM vorinostat on MCF7 for 6 hours

6100 instances over 1309 drugs

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Cel l T ype

Drug

Do sag e

2008 price: $250 US

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Lamb, J et al. 2006. “The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.” Science 313(5795):

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Lamb, Justin. 2007. “The Connectivity Map: a new tool for biomedical research.” Nature Reviews Cancer 7(1): 54–60.

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http://www.broadinstitute.org/cmap/

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Drug-Drug similarity

Input: 13 HDAC gene signature

Lamb, J et al. 2006. “The Connectivity Map: using gene-expression signatures to connect small

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Drug-disease

Sirolimus reverses gluco-corticoid resistance in acute lymphoblastic leukemia.

Lamb, J et al. 2006. “The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.” Science 313(5795): 1929–1935.

Dexamethasone only

Dexamethasone + Sirolimus

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Sample Calculation

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Kolmogorov-Smirnov statistics

The score captures the

maximum derivation from the random distribution.

0 0.25 0.5 0.75 1

1⁰ 2 3 4 5

0.1

0.5

0.8

0.9

0.2

0.4

0.6

0.8

1

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213731_s_at 208793_x_at 208711_s_at 208623_s_at

203725_at

200965_s_at 201540_at 215677_s_at 205472_s_at

204802_at

Sample calculation

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-‐0.608

Raw score calculation

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Score

•  t: number of tags

•  n: total number of tags (22283)

•  score = a if a >b

•  score = -b if b>a

b =13542/22283 - 0/5 = 0.608 a = 4/5 - 2801/22283 = 0.674

-‐0.608

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Drug ranking

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Enrichment

• t: number of instances

• n: total number of instances (6100)

5171/6100 - 0/1 = 0.848

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Permutation

p-value is estimated through permutation analysis by

constructing empirical null

distribution.

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http://rlv.zcache.com/my_p_value_is_smaller_than_your_p_value_tshirt-rdb18d031a5774ce18f1a42edfe212916_804gs_512.jpg