J. Fernebro, P. Francis, P. Edén, Å. Borg, I. Panagopoulos,

F. Mertens, J. Vallon-Christersson, M. Åkerman, N. Mandahl,

M. Nilbert

Departments of Oncology, Theoretical Physics, Clinical Genetics, and Pathology

Lund University, Sweden

Princy.Francis@onk.lu.se

Gene expression profiles relate to gene fusiontype and metastasis in synovial sarcoma

Aims

Groups of genes discriminating the monophasic from biphasic

have been previously identified

(Allander et al., 2002; Nagayama et al., 2002)

Do gene expression profiles in synovial sarcoma correlate with: Histopathology Cytogenetics Gene fusion type Metastatic potential

23 synovial sarcoma specimens from 21 patientsmean age 46, 12 males, 16 primary tumors, 3 local recurrences, 4 metastases

Histopathology monophasic (17) vs biphasic (4)

Cytogenetics t(X;18) (4) vs complex karyotype (12)

Gene fusion type SS18/SSX1 (12) vs SS18/SSX2 (7)

Metastatic potential metastasis (13) vs metastsis-free (5)

SS18 SSX

Material

Scan

Process Image

Labelled cDNA

18-20 hrs incubation at 42oC

Hybridize to microarray slide

Reference RNA

Tumour RNA

Image and

Data Analysis

cDNA microarray, 27648 IMAGE clones25648 distinct reporters17517 unique UniGene clusters

Hierarchical clusteringbased on ~5800 genes

- Unsupervised

- Supervised Golub scores, random permutation tests

Methods

Expression profiles did not relate to histopathology or karyotype

Significant discriminators for gene fusion type and metastatic potential

Metastasis No Yes

Gene fusion type Type 1 Type 2

Supervised clustering

Up SS18/SSX1 - TCF7 - LEF1 - RTP801 - CKB - NOTCH2 - Metallothioneins

Up SS18/SSX2- BENE - MN1- NEDD4 - FRAG1- MSX2 - TIEG

Gene fusion type

Transcription factors

Signalling molecules

Multiple metallothioneins

Discriminating genes

Up metastasis- TYMS - TOP2A- PTTG1 - IGFBP2- BUB1 - COL18A1

Up without metastasis- ProSAPiP1 - TNNT1- ICAM1 - DDX21- FRAG1 - TCF8

Metastatic potential

Cell proliferation

Cell cycle progression

Transcriptional regulation

45 from top 200 common to both lists Up in metastasis also up in SS18/SSX1

- BSG - FRAG1- NOTCH2- RGS2- TCF7 - TCF8

Common discriminators

Up SS18/SSX1 - TCF7 - LEF1 - RTP801 - CKB - NOTCH2 - Metallothioneins

Up SS18/SSX2- BENE - MN1- NEDD4 - FRAG1- MSX2 - TIEG

Gene fusion type

Up metastasis- TYMS - TOP2A- PTTG1 - IGFBP2- BUB1 - COL18A1

Up without metastasis- ProSAPiP1 - TNNT1- ICAM1 - DDX21- FRAG1 - TCF8

Metastatic potential

Discriminating genes

Targets for chemotherapeutic drugs

Up SS18/SSX1 - TCF7 - LEF1 - RTP801 - CKB - NOTCH2 - Metallothioneins

Up SS18/SSX2- BENE - MN1- NEDD4 - FRAG1- MSX2 - TIEG

Gene fusion type

Up metastasis- TYMS - TOP2A- PTTG1 - IGFBP2- BUB1 - COL18A1

Up without metastasis- ProSAPiP1 - TNNT1- ICAM1 - DDX21- FRAG1 - TCF8

Metastatic potential

Discriminating genes

Previously reported in synovial sarcoma

Up SS18/SSX1 - TCF7 - LEF1 - RTP801 - CKB - NOTCH2 - Metallothioneins

Up SS18/SSX2- BENE - MN1- NEDD4 - FRAG1- MSX2 - TIEG

Gene fusion type

Up metastasis- TYMS - TOP2A- PTTG1 - IGFBP2- BUB1 - COL18A1

Up without metastasis- ProSAPiP1 - TNNT1- ICAM1 - DDX21- FRAG1 - TCF8

Metastatic potential

Discriminating genes

Previously reported in metastasizing tumors

Up SS18/SSX1 - TCF7 - LEF1 - RTP801 - CKB - NOTCH2 - Metallothioneins

Up SS18/SSX2- BENE - MN1- NEDD4 - FRAG1- MSX2 - TIEG

Gene fusion type

Up metastasis- TYMS - TOP2A- PTTG1 - IGFBP2- BUB1 - COL18A1

Up without metastasis- ProSAPiP1 - TNNT1- ICAM1 - DDX21- FRAG1 - TCF8

Metastatic potential

Discriminating genes

Differentially expressed genes relative to gene fusion type and metastatic potential in synovial sarcoma

Signaling molecules, transcription factors and metallothioneins among the fusion type discriminating genes

Known targets for chemotherapy (TYMS and TOP2A) upregulated in metastasizing tumors

Conclusions