Deficient homologous recombination DNA repair appears to cluster sarcoma patients sensitive to trabectedin (ET-743, Yondelis®)

Maki RG, Taron M, van Oosterom AT, Schöffski P, Tercero JC, Fernandez Sousa-Faro JM, Jimeno JM, Rosell R

Memorial Sloan Kettering Cancer Center, New York, NY;  Hospital Germans Trias i Pujol, Badalona, Barcelona, SPAIN 

UZ Gasthuisberg, Leuven, BELGIUMPharmaMar Research and Development, Madrid, SPAIN

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E. turbinata

Introduction

ET-743 (trabectidin, Yondelis®) is a marine-derived compound in phase II-III development for solid tumors Binds to the minor groove of DNA Interacts with transcription factors and DNA binding proteins Disorganizes of the microtubule network Perturbs the cell cycle Interferes with DNA repair pathways

Van Kesteren et al. Anticancer Drugs. 2002; 13:381

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ET-743 induces long-lasting responses and tumor control in a clinically relevant proportion of patients.

26%29%OS > 2 years (percent)

10.110.3MEDIAN OS (months)

22%20%PFS > 6 months

15 (24%)41 (22%)TUMOR CONTROL

5 (8%)13 (7%)SD

4 (6%)14 (8%)MR

6 (10%)14 (8%)PR

Dox / Ifos Resistant (n=63)Full Cohort (n=183)

PARAMETER

JA López et al. Proc. ASCO 2003; Abstr. 3293A. Le Cesne et al, JCO 2005; 23:576

ET-743 sarcoma program: combined phase II results

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Supervivencia Global – ET- 743 STSMedian Survival 10.3 months

29% of pts alive > 2 yrs

ET-743 phase II sarcoma program: Overall survival

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Identify and validate molecular markers that correlate with sensitivity or resistance to ET-743

– Select the group of STS patients who will most benefit from ET-743

Marker +

Marker -

Objective

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• Human STS cell lines explanted from chemotherapy-naïve patients• 12 low passage sarcoma cell lines sensitive or resistant to ET-743 underwent

gene expression profile (CNIO Oncochip; > 6700 cancer related genes)

STS cell lines

10nM ET-743

0h 6h 12h 24h 72h

MOLECULAR PROFILE OF ET-743

I. Identification of genes in vitro associated with ET-743 sensitivity or

resistance

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51EWING SARCOMASR2910

150.4OSTEOSARCOMASR0312

440.7LIPOSARCOMA SR2103/B

450.7LIPOSARCOMA SR2103/A

>3000.5LIPOSARCOMASW872

>3009LEIOMYOSARCOMALS0904

60

10

not done

>300

14

21.5

Doxorubicin

(nM)

>100WILMS TUMORRS0306

1EWING SARCOMAA673

>100

>100

1

0.4

ET-743

(nM)

MPNST

MPNST

FIBROUS TUMOR

LEIOMYOSARCOMA

TUMOR HISTOLOGY

SR0406

SR2410

SR2205

CA1010

CELL LINE

Chemotherapy sensitivity profile of low passage sarcoma cell lines

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Genes differentially expressed in ET-743 sensitive and resistant cell lines

• Cell cycle control – TP53

• Inhibition of transcription and the DNA damage response– JUNB, ATF3, CS-1, SAT, ID2, GADD45B

• DNA repair– BRCA1, XPD, RAD17, p31, p53DINP1

9Takebayashi Y. et al. Nature Med 2001; 7:961

II. DNA repair genes appear central to the function of ET-743: gene deletion experiments

Intactnucleotide

excision repairincreases

cytotoxicity

Deficientdouble stranded

break repairincreases

cytotoxicity

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III. Examining genes involved in DNA repair and how they are implicated in

patient responses to ET-743

• Source material: tumor samples from 45 heavily pre-treated STS patients, subsequently treated with ET-743

• Analyze genes important in DNA repair by mRNA expression and / or analysis of single nucleotide polymorphisms (SNPs)

(a) NER pathway: ERCC1 and XPD mRNA expression and SNP analysis

(b) BRCA1 mRNA expression

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# Pts PR MR SD(*) PD

45 5 1 14 25

53 patients, 8 not evaluable;Median Duration of PR or MR: 13.3 months

(*) 4 / 14 SD achieved PFS > 6 mo 10 / 45 PD achieved PFS > 6 mo

Best ET-743 response in patients providing tumor samples

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Overall survival Progression-free survival

Median: 11.8 months Median: 1.6 monthsPFS > 6 months: 26 %

73% of this group were compassionate use patients:

Histology: Leiomyosarcoma 31%Osteogenic sarcoma 22%

Synovial sarcoma 16%

Prior chemo: Median # Regimens Median # Agents

2 (0-6) 2 (0-10)

Comparison of this cohort to the larger cohort of analyzed patients

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Paraffin embedded

tumor tissue

RNA extraction DNA extraction

Quantitation ofRNA expression level

Identification ofpolymorphic DNA

alleles

Reverse transcriptionQ-RT-PCR

Allele discriminationRT-PCR

Gln

NTC

Gln/Gln

Lys/Gln

Lys/Lys

Lys

Gln XPD 751 Gln

Lys XPD 751 Gln

Lys XPD 751 Lys

Experimental design

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Polymorphism

Patients

PR

Lys751Lys

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3 Asp312Asp 15 3

Gln751Gln 5 0 Asn312Asn 7 0

There is a trend in the association between Lys751Lys and Asp312Asp genotypes in XPD gene and better clinical response to ET-743 in sarcoma patients (but p=NS by Fisher’s exact test).

XPD polymorphisms associated with responses to ET-743

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high

low

high

low

Cut-off expression level = 5.86 Cut-off expression level = 1.95

Patients with high levels of expression of both ERCC1 and XPDshow trend toward better tumor control rates ( PFS > 6 months )

p=NS by Fisher’s exact test

PFS by ERCC1 PFS by XPD

High or low ERCC1 and XPD expression and their association with overall survival

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Parameter

ERCC1 mRNA

Expression Levels

< median > median

PR + MR / Total (%)

2 / 19 (11%)

4 / 19 (21%)

PFS > 6 months 3 / 19 (16%) 6 / 19 (32%)

Patients with high levels of ERCC1 expression showed a trend toward better RR (21% vs. 11%) and a higher

rate of patients achieving PFS > 6 months (32% vs 16%)(p = NS by Fisher exact test)

ERCC1 expression and sensitivity to ET-743

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Parameter

BRCA1 expression levels

< median > median

PR + MR (%)PFS > 6 months (%)

4 / 17 (24%) 6 / 17 (35%)

1 / 17 (6%)*1 / 17 (6%)++

Patients with low BRCA1 mRNA expression levels demonstrated a trend towards higher PR+MR and tumor control rates

*p = 0.3 ++p = 0.08

BRCA1 expression and ET-743 sensitivity

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Median survival:

BRCA1 < median: 16.8 monthsBRCA1 > median: 6.0 months

Total population: 11.8 monthsPhase II pivotal: 10.3 months

PFS > 6 month rate:

BRCA1 < median: 41 %BRCA1 > median: 6 %

Total population : 26 %Phase II pivotal: 20 %

p = 0.02p = 0.06

Low

Low

SurvivalPFS

HighHigh

Kaplan-Meier survival curves by BRCA1 expression

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Conclusions

• Preclinical analysis of cell lines sensitive or resistant to ET-743 identifies a set of genes that underscores the importance of DNA repair (intact NER) in the mechanism of action of ET-743.

• Low expression of BRCA1 is associated with better objective response, higher rate of progression free survival at 6 months, and a statistically significant improved median survival of sarcoma patients treated with ET-743.

• High expression levels of XPD or ERCC1 may be associated with improved clinical outcome on ET-743

• Lys751Lys and Asp312Asp genotypes in the XPD gene also appear to be associated with a higher rate of response to ET-743.

• Analysis of a larger group of tumors from patients sensitive and resistant to ET-743 will be necessary to confirm the relationship between DNA repair genes and ET-743 sensitivity.

20Positano, Italy

Thank you for the opportunity to present.