Cancer Research GroupJoanne Chen

Yuh-Shan Jou

You-Di Liao

Konan Peck

Steve R. Roffler

Sheau-Yang Shieh

Tsann-Long Su

Cheng-Wen Wu

Pan-Chyr Yang

Joint appointment, NHRI

Joint appointment, NTUH

Cancer Research Group

A pipeline integration of technology development, basic, applied, and clinical studies

Genomic & proteomic research tool developments

Molecular pathogenesis studiesCarcinogenesis & metastasis

Identification of biomarkersfor diagnosis, prognosis and therapy

Therapeutic agents and clinical assays development

Clinical validation

Bench

Bedside

Genomic and proteomic research tool developments

Directed molecular evolution tocreate new therapeutic proteins

(Steve Roffler)

family of mutants

error-prone PCR

Negative mutationsPositive mutations

Retroviral transduction of fibroblasts

Flow Cytometer sortingfor activity at neutral pH

random fragmentation

PCR recovery

DNA assembly

human beta-glucuronidase

Surface expressed proteins for therapy and imaging

(Steve Roffler)

TMLS

cytokineantibody

enzyme

Aptamer arrays for protein-specific expression profiling

(Konan Peck)

Bioinformatics tools and databasefor hepatocarcinoma oncogenomics

(Yuh-Shan Jou)

High throughput transcript-specific expression profiling system

(Konan Peck)

CL1-0 CL1-1 CL1-5 CL1-5-F40

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Model cell lines & multi-well assay for cancer cell invasion studies

(Pan-Chyr Yang & Cheng-Wen Wu)

Molecular pathogenesis studies (carcinogenesis)

-Genetic events associated with pathogenic development of GI-track cancers Rho GTPases & Wnt/-catenin/TCF pathway

Cancer genomics & tumor biology of GI-track cancer (Joanne Chen)

Identify and study human hepatocellular carcinoma genes by genomic approaches (Yuh-Shan Jou)

- HCC genes somatic mutation screening- Homozygous deletion of chromosome 13q12.11- Integrated HCC database: OncoDB.HCC for bioinformatics analysis

Genome-wide minimal deleted regions, two major tumorigenic pathways,and a homozygous deletion of 13q12.11 in HCC have been identified.

1. Overexpression of RTKN, a Rho GTPase effector, contributes to GC pathogenesis, and its overexpression is associated with GC progression.2. Abnormal expression of OPN and its receptor CD44 contributes to cancer progression.

p53 and cell cycle checkpoints (Sheau-Yann Shieh)

- The role of CHK1, CHK2-interacting proteins in checkpoint control- The role of CHK1 and CHK2 in DNA double strand break repair

Mol. Biol. Cell 16:1684-1695, 2005

p53

J. Biol. Chem. 280: 7748-7757, 2005

Molecular pathogenesis studies (carcinogenesis)

Pathogenesis of human cytomegalovirus (Cheng-Wen Wu)

- The functions of the HCMV IE2 protein

1. DNA methylation may be involved in the regulation of the HCMV major IE promoter2. TE2, a novel protein acetyltransferase that interacts with HCMV IE2, increases the act

ivity of the DNA methyltransferase 1

Molecular pathogenesis studies (metastasis)

- Genome-wide identification of metastasis related genes (Pan-Chyr Yang & Konan Peck)

- Characterize novel and known invasion/metastasis suppressors and enhancers: CRMP-1, HLJ1, LCRMP-1, Slug (Pan-Chyr Yang); TAL6 (Steve Roffler) KLK8 (Konan Peck)

- Identification of metastasis-related proteases and protease inhibitors (Cheng-Wen Wu)

CRMP-1

PPG to decipher the molecular mechanism of cancer metastasis

706050403020100

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Time in months

KLK8 high

KLK8 low

P = 0.019

N=33

N=22

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Clinical studiesCell biology studies Histology studies Mouse model studies

Empirical approaches for validation and characterization

Biomarkers identified in the research projects

In silico database search Empirical genomic approaches

Candidate marker genes

Biomarkers

Validation with cancer cell lines

Validation with clinical specimens

Validation with mouse models

Metastasis and prognosis biomarkers: CRMP-1, LCRMP-1, HLJ1, Slug, KLK 8 TAL6, CD13, CD44, RTKN, OPN

Cancer therapy efficacy assessment markers: KRT19, UCHL1, FN1, TRIM28

Drug target for metastasis inhibition: LCRMP-1, Slug

Anti-tumor Ribonucleases from Bullfrogs(You-Di Liao)

OOH

HOOH

CO

OH

O

N

N

O

O

HO O

O

O

NH

9-ACG

G

N

N

O

O

HO O

NH

O+

-CO2

9-AC

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Glucuronide prodrugs for cancer therapy(Steve Roffler)

BO-0742N

HN

OCH2CH2N(CH2CH2Cl)2

CH2OH

N

HN

R2 R1

NH2

Me, OMe

5-(9-acridinylamino)toluidines5-(9-Acridinylamino)anisidines

N

N

R

OH O

O

Gene alkylating agents(in preclinical studies)

Topoisomerase II Inhibitors (9-Anilinoacridine Analogues)

• Topoisomerase I Inhibitors (Camptothecin Analogues)

Discovery and Development of Potential Anticancer Agent(Tsann Long Su)

Therapeutic agent developments

Clinical assay developments

Microarray for prognosis of NSCLC patients(Pan-Chyr Yang)

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Relative intensity

Serine/threonine-protein kinase MAK (2)KIAA0230 gene ( ACC.:AA101407)

Cytochrome C oxidase polypeptide VAMetallothionein-IA (1)

Tropomyosin alpha chain (3)Calcyclin

ATP synthase D chain, mitochondrial (1)Metallothionein I-B gene

Metallothionein isoform 2ITBA1 protein

Metallothionein I-F geneKIAA0134 gene ( ACC.: R48810)

Zinc finger protein HRX (1)High-mobility group protein

HPV type 5, E6/E7HnRNP F protein

Protein disulfide isomerase-related protein (3)Autoantigen calreticulin

Hypothetical 29.2 kD protein (1)Heme-regulated EIF-2-alpha kinase (1)

Homeobox protein PRHKIAA0276 gene ( ACC.: H83832)

Guanine nucleotide-binding protein (1)Casein kinase I gamma 2

Long-chain-fatty-acid-coA ligase (1)Actin, alpha (1)

Tumor-associated antigen L6Disintegrin-metalloprotease

Acyl-coA desaturase 1 (2)

CL1-0CL1-1CL1-5CL1-5-F4RT4EJT24

Metastasis associated genes

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Relative intensity

Serine/threonine-protein kinase MAK (2)KIAA0230 gene ( ACC.:AA101407)

Cytochrome C oxidase polypeptide VAMetallothionein-IA (1)

Tropomyosin alpha chain (3)Calcyclin

ATP synthase D chain, mitochondrial (1)Metallothionein I-B gene

Metallothionein isoform 2ITBA1 protein

Metallothionein I-F geneKIAA0134 gene ( ACC.: R48810)

Zinc finger protein HRX (1)High-mobility group protein

HPV type 5, E6/E7HnRNP F protein

Protein disulfide isomerase-related protein (3)Autoantigen calreticulin

Hypothetical 29.2 kD protein (1)Heme-regulated EIF-2-alpha kinase (1)

Homeobox protein PRHKIAA0276 gene ( ACC.: H83832)

Guanine nucleotide-binding protein (1)Casein kinase I gamma 2

Long-chain-fatty-acid-coA ligase (1)Actin, alpha (1)

Tumor-associated antigen L6Disintegrin-metalloprotease

Acyl-coA desaturase 1 (2)

-100 -80 -60 -40 -20 0 20 40 60 80 100

Relative intensity

Serine/threonine-protein kinase MAK (2)KIAA0230 gene ( ACC.:AA101407)

Cytochrome C oxidase polypeptide VAMetallothionein-IA (1)

Tropomyosin alpha chain (3)Calcyclin

ATP synthase D chain, mitochondrial (1)Metallothionein I-B gene

Metallothionein isoform 2ITBA1 protein

Metallothionein I-F geneKIAA0134 gene ( ACC.: R48810)

Zinc finger protein HRX (1)High-mobility group protein

HPV type 5, E6/E7HnRNP F protein

Protein disulfide isomerase-related protein (3)Autoantigen calreticulin

Hypothetical 29.2 kD protein (1)Heme-regulated EIF-2-alpha kinase (1)

Homeobox protein PRHKIAA0276 gene ( ACC.: H83832)

Guanine nucleotide-binding protein (1)Casein kinase I gamma 2

Long-chain-fatty-acid-coA ligase (1)Actin, alpha (1)

Tumor-associated antigen L6Disintegrin-metalloprotease

Acyl-coA desaturase 1 (2)

CL1-0CL1-1CL1-5CL1-5-F4RT4EJT24

Metastasis associated genes

Rapid assessment of therapy efficacy and relapse detection method(Konan Peck & Pan-Chyr Yang)

Circulating tumor cell detectionCirculating tumor cell detection

Leukocytes

Polymerase chain reaction

Tumor cell

Skin

Connective tissue

Case 4: Stage IV NSCLC patient

-2

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-2

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2

4

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Survival: 8.6 month

2/d-1

Case 3： Stage IIIb NSCLC patient

Lc

-2

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2

4

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1/d7 2/d5

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Survival: 60.8 months

Case 4: Stage IV NSCLC patient

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Survival: 8.6 month

2/d-1

Case 3： Stage IIIb NSCLC patient

Lc

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Survival: 60.8 months

Microarray for subtyping of gastric cancers(Joanne Chen)

Using marker genes to detect the amount of circulating tumor cells before and after the treatment allows rapid efficacy assessment and relapse detection.

Achievements in the past 5 years

Publications in academic journals Technology transfer to biotech industry

Publications in basic research journals

American Journal of Respiratory Critical Care Medicine American Journal of PathologyCancer ResearchJournal of Biological ChemistryJournal of the National Cancer Institute Molecular Biology of the Cell Oncogene The EMBO Journal . . .

Publications in applied or clinical research journalsBioinformaticsClinical Cancer ResearchJournal of Clinical OncologyNew England Journal of MedicineNucleic Acids Research . . .

Achievements in the past 5 years

Multi-national intellectual property rights

Granted patentsK. Peck, et al. (2001) US Patent # 6,218,114 K. Peck, et al. (2001) ROC patent 438889K. Peck, et al. (2002) European Patent EP 0822261K. Peck, et al. (2003) ROC patent 541340 S.R. Roffler, et al. (2003) US Patent # 6,596,849S.R. Roffler, et al. (2003) US Patent # 6,617,118S.R. Roffler, et al. (2003) European Patent EP 0990661S.R. Roffler, et al. (2004) US Patent # 6,699,972S.R. Roffler, et al. (2004) ROC Patent 205511T.L. Su, et al. (2004) US Patent # 6,821,983 K. Peck, et al. (2005) US Patent # 6,867,050K. Peck, et al. (2005) ROC patent I232867

Pending patent applicationsP.C. Yang, et al. (2003) European Patent 1271153 A2P.C. Yang, et al. (2003) US Patent # 20030077624 A1.P.C. Yang, et al. (2003) European Patent 1285970 A2P.C. Yang, et al. (2003) US Patent # 20030054387 A1.S.R. Roffler, et al. (2004) US Patent # 20040014156 A1.T.L. Su, et al. (2004) US Patent # 20040198765 A1.P.C. Yang, et al. (2005) US Patent # 20050182016 A1.Y.D. Liao, et al. (2005) US Patent # 20050214899 A1.

Technology transfers to biotech industry

1. S.R. Roffler, et al. “Monoclonal antibody against polyethylene glycol” to Bayer and Hoffmann-LaRoche2. K. Peck, et al. “Method for profiling gene expression pattern and isolation of differentially expressed genes” to Taiwan Genome Sciences, Inc. and 4 other companies.3. K. Peck, et al. “Method for constructing high-density non-redundant gene arrays” to Taiwan Genome Sciences, Inc. and 2 other companies. 4. K. Peck, et al. “Methods for rapid antimicrobial susceptibility testing” to Cold Spring Biotech, Inc.5. P.C. Yang, et al. “Metastasis-associated genes” to AdvPharma, Inc.6. P.C. Yang, et al. “Collapsin response mediator protein-1 as tumor metastasis marker” to AdvPharma, Inc.