Signature-based small molecule screening identifies cytosine arabinoside as an EWS/FLI modulator in Ewing sarcoma.
BACKGROUND
The presence of tumor-specific mutations in the cancer genome represents a potential opportunity for pharmacologic intervention to therapeutic benefit. Unfortunately, many classes of oncoproteins (e.g., transcription factors) are not amenable to conventional small-molecule screening. Despite the identification of tumor-specific somatic mutations, most cancer therapy still utilizes nonspecific, cytotoxic drugs. One illustrative example is the treatment of Ewing sarcoma. Although the EWS/FLI oncoprotein, present in the vast majority of Ewing tumors, was characterized over ten years ago, it has never been exploited as a target of therapy. Previously, this target has been intractable to modulation with traditional small-molecule library screening approaches. Here we describe a gene expression-based approach to identify compounds that induce a signature of EWS/FLI attenuation. We hypothesize that screening small-molecule libraries highly enriched for FDA-approved drugs will provide a more rapid path to clinical application.


RESULTS
A gene expression signature for the EWS/FLI off state was determined with microarray expression profiling of Ewing sarcoma cell lines with EWS/FLI-directed RNA interference. A small-molecule library enriched for FDA-approved drugs was screened with a high-throughput, ligation-mediated amplification assay with a fluorescent, bead-based detection. Screening identified cytosine arabinoside (ARA-C) as a modulator of EWS/FLI. ARA-C reduced EWS/FLI protein abundance and accordingly diminished cell viability and transformation and abrogated tumor growth in a xenograft model. Given the poor outcomes of many patients with Ewing sarcoma and the well-established ARA-C safety profile, clinical trials testing ARA-C are warranted.


CONCLUSIONS
We demonstrate that a gene expression-based approach to small-molecule library screening can identify, for rapid clinical testing, candidate drugs that modulate previously intractable targets. Furthermore, this is a generic approach that can, in principle, be applied to the identification of modulators of any tumor-associated oncoprotein in the rare pediatric malignancies, but also in the more common adult cancers.
Stegmaier
Kimberly
K
Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, United States of America.
Wong
Jenny S
JS
Ross
Kenneth N
KN
Chow
Kwan T
KT
Peck
David
D
Wright
Renee D
RD
Lessnick
Stephen L
SL
Kung
Andrew L
AL
Golub
Todd R
TR
D000818:Animals; D000964:Antimetabolites, Antineoplastic / Q000494:pharmacology* / Q000627:therapeutic use; D001859:Bone Neoplasms / Q000188:drug therapy* / Q000235:genetics / Q000473:pathology; D045744:Cell Line, Tumor; D003561:Cytarabine / Q000494:pharmacology* / Q000627:therapeutic use; D016503:Drug Delivery Systems; D004354:Drug Screening Assays, Antitumor / Q000379:methods*; D005456:Fluorescent Dyes / Q000032:analysis; D005470:Fluorometry; D005784:Gene Amplification; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D006801:Humans; D051379:Mice; D008863:Microspheres; D015394:Molecular Structure; D008970:Molecular Weight; D015514:Oncogene Proteins, Fusion / Q000096:biosynthesis / Q000187:drug effects* / Q000235:genetics; D051789:Proto-Oncogene Protein c-fli-1; D034622:RNA Interference; D034802:RNA-Binding Protein EWS; D012512:Sarcoma, Ewing / Q000188:drug therapy* / Q000235:genetics / Q000473:pathology; D014157:Transcription Factors / Q000096:biosynthesis / Q000187:drug effects* / Q000235:genetics; D023041:Xenograft Model Antitumor Assays
D000964:Antimetabolites, Antineoplastic; C106031:EWS-FLI fusion protein; D005456:Fluorescent Dyes; D015514:Oncogene Proteins, Fusion; D051789:Proto-Oncogene Protein c-fli-1; D034802:RNA-Binding Protein EWS; D014157:Transcription Factors; D003561:Cytarabine