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Yves Pommier, M.D., Ph.D.

Portait Photo of Yves Pommier
Laboratory of Molecular Pharmacology
Head, DNA Topoisomerase/Integrase Group
Laboratory Chief
Building 37
Room 5068
Bethesda, MD 20892-4255
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Dr. Pommier received his M.D.and Ph.D.degrees from the University of Paris, France, and has been at the NIH since 1981. Dr. Pommier is a member of the Molecular Target steering committee at the NCI. He received an NIH Merit Award for his role in elucidating the function of topoisomerase enzymes as targets for anticancer drugs and Federal Technology Transfer Awards for studies on HIV-1 integrase and DNA topoisomerase inhibitors. Dr. Pommier is a program committee member of the American Association for Cancer Research, Senior Editor for Cancer Research, and associate editor for Cancer Research, Molecular Pharmacology, Leukemia, The Journal of Experimental Therapeutics and Oncology, The International Journal of Oncology, and Drug Resistance Updates. Dr. Pommier holds several patents for inhibitors of DNA topoisomerases I and II and HIV-1 integrase inhibitors.


DNA, Topoisomerases, Checkpoints, and HIV Integrase Molecular Pharmacology

DNA topoisomerases are essential for all DNA transactions due to the duplex helical structure of DNA. They change the DNA topological structure by introducing reversible breaks in the DNA, which are referred to as cleavage complexes. We recently discovered a novel gene for a specific mitochondrial topoisomerase I, which demonstrate that human cells contain six topoisomerases genes: two for the type I topoisomerases (TOP1 and TOP1mt), two for the type II (TOP2-alpha and TOP2-beta) and two for the type III topoisomerases (TOP3-alpha and TOP3-beta). We are pursuing these studies in other species, and preliminary results indicate that mitochondrial Top1 (Top1mt) is present and restricted to all vertebrates whose genome has been sequenced to date, and that the structure of TOP1mt gene is remarkably conserved when compared to the nuclear TOP1 gene, suggesting that both genes derived from duplication of a common ancestor gene that may have encoded both mitochondrial and nuclear type I topoisomerases.

Top1 and Top2 are targets for the most potent anticancer drugs to date. Top2 inhibitors include the widely used anticancer agents VP-16, adriamycin and mitoxantrone. Camptothecin is a specific Top1 inhibitor, and several camptothecin derivatives have recently been introduced in the clinic with promising results in solid tumors including colon, lung and ovarian carcinomas. Our aims regarding topoisomerase inhibitors are to discover novel inhibitors, and to study the molecular interactions between drugs, DNA and the enzyme-DNA complexes, as well as the cellular determinants of selectivity of cancers. We have shown that camptothecins bind at the Top1-DNA interface. This mode of non-competitive inhibition (consisting of a trimer: the drug, the DNA, and Top1) represents a pharmacological paradigm, as the camptothecin molecule blocks a functional complex between the DNA and Top1 (by extension: two macromolecules) by inhibiting its dissociation rather than by blocking its formation. It is noteworthy that the later approach is most commonly sought in current development of inhibitors of macromolecular interactions, and that, based of the camptothecin paradigm, we would propose considering inhibitors of macromolecular dissociation as well. We have sequenced TOP1 point mutations that render the enzyme resistant to camptothecins, and structural studies are ongoing to further elucidate the structure of the Top1-DNA-camptothecin ternary complex. Such structures will be used for rational design of novel Top1 poisons.

We have recently found that Top1-mediated DNA damage can be elicited by commonly occurring endogenous DNA modifications (mismatches, abasic sites, 8-oxoguanine, DNA breaks), as well as by carcinogenic polycyclic aromatic adducts (ethenoadenine, benzo[a]pyrene diol epoxide adducts). These observations suggest that frequently occurring DNA modifications can lead to the formation of Top1 cleavage complexes. We are investigating the mechanisms of damage and repair in several ways: (1) characterization of the cellular lesions induced by Top1 cleavage complexes in cancer cells (replication-mediated DNA double-strand breaks); (2) elucidation of the cellular responses/pathways elicited in response to such lesions (activation of DNA-PK, RPA phosphorylation, activation of histone phosphorylation [gamma-H2AX], transcriptional responses); (3) analysis of the effects of camptothecins in mammalian cells with known genetic defects (Werner syndrome and cells deficient in PARP, beta-polymerase, XRCC1, etc.); and (4) investigation of the biochemical processing of Top1 cleavage complexes in vitro using oligonucleotides and purified repair factors (such as TDP and PNKP). To understand how the genetic makeup of human cells influences their cellular response to anticancer agents and the rationale for the selectivity of topoisomerase inhibitors toward cancer cells, we are studying cell lines from the NCI Anticancer Drug Screen and cell lines with selected gene disruptions.

Ecteinascidin 743 (Et743) is a natural product (from a Caribbean marine tunicate) remarkably active against sarcomas and presently in phase I/II clinical trials. Because of its unique activity profile, we are elucidating its mechanism of action. We first demonstrated that Et743 alkylates guanine N2 at selective sites in the DNA minor groove. This observation sets Et743 apart from the DNA alkylating agents currently in clinical use. We recently generated Et743-resistant cells, and found that these cells are deficient in nucleotide excision repair (NER). Additional studies led to the hypothesis that Et743 traps the transcription-coupled repair machinery as it attempts to remove the Et743-DNA adducts. Thus, Et743 is not just a Top1 and a transcription inhibitor, but its antiproliferative activity appears dependent upon TC-NER. To our knowledge, Et743 is the first drug with such a mechanism of action. This mechanism of action is opposite to cisplatin's, which is selectively toxic to TC-NER-deficient cells. A translation program has been initiated to evaluate by proteomic analysis the relationship between TC-NER factors and therapeutic response to Et743 and cisplatin.

Our laboratory has pioneered the HIV integrase inhibitor research since 1993. We investigate the molecular interactions of drugs with retroviral integrases using recombinant integrases in biochemical assays and by exploring different steps of the integration reaction. The rationale for searching HIV integrase inhibitors is that: (1) viruses with mutant integrase cannot replicate, and (2) integrase is one of the three retroviral enzymes (with reverse transcriptase and protease) with no cellular equivalent. Our goals are to discover new antiviral agents, evaluate which steps of the integration reactions are affected by drugs, and determine the drug binding site in the HIV-1 integrase-DNA complex. Discovery and studies of HIV integrase inhibitors will provide new strategies for anti-AIDS therapy.

This page was last updated on 1/23/2009.