- Email: [email protected]
Gene regulation and cancer
MEETING REPORTS
Bioinformatics in Siberia
structural properties of whole genomes. Oral presentations were complemented by about 80 posters, detailing a wealth of specialized databases, computer programs and models, attesting to the vitality of the field both in Russia and across the world. We refer the reader to the web page containing links to all the relevant information, including the full program of the meeting and abstracts2. Full proceedings of the conference can be ordered from Nikolay Kolchanov ([email protected]). Finally, a selection of papers will be published in a forthcoming special issue of Bioinformatics. As the meeting unfolded, Russia was sinking deeper into political and economic crisis. The situation for Russian scientists is becoming ever more difficult. Salaries are hardly paid, and in any case, have lost much of their already low value. Payment of grants has often been suspended. Basic experimental materials are scarce, and in some institutes, even telephone and fax lines have been cut off because of the lack of money. In such a
Outlook
problematic context, bioinformatics constitutes an interesting alternative. Indeed, with electricity, a few computers, and access to the web, Russian scientists can face economic and political adversities and pursue their research. The visit to the Institute of Cytology and Genetics in Novosibirsk gave us a striking demonstration that Russian scientists are far from giving up and are courageously looking for every way to do interesting science. To support these efforts, the best we can do is publicize their achievements and, whenever possible, engage in fruitful international collaborations. The results of a number of such collaborations were presented at the conference.
Further reading 1 Ashburner, M. and Goodman, N. (1997) Informatics – genomes and genetic databases. Curr. Opin. Genet. Dev. 7, 750–756 2 Bioinformatics of Genome Regulation and Structure, http://bgrs.bionet.nsc.ru
Gene regulation and cancer Gene Regulation and Cancer: 10th Anniversary Meeting of the American Association of Cancer Research Special Conferences in Cancer Research, The Homestead, Hot Springs, Virginia, USA, 14–18 October 1998. Ten years ago, Phillip Sharp (MIT, USA) and Steven McKnight (UT Southwest Medical Center, USA) organized the first AACR Special Conference in Cancer Research on the subject of ‘Gene Regulation and Cancer’. With the support of a major educational grant from Janssen Pharmaceutica and the Janssen Research Foundation, Sharp, McKnight and Jacqueline Lees (MIT, USA) convened another AACR Special Conference on the same topic. This year’s conference dramatically illustrated the advances of the past decade over a broad front ranging from analysis of protein structure to clinical trials for new therapeutics. An important topic of the conference was the functions of oncogenes and tumor suppressors in cell proliferation and development. For example, Jacqueline Lees (MIT, USA) described the E2F family of transcriptional activators and illustrated, through phenotypic analysis of transgenic mice, that E2F4 (the major E2F form in vivo) plays a crucial role in the terminal differentiation of hemopoietic cell lineages. Nikola Pavletich (Memorial Sloan-Kettering Cancer Center, USA), through high-resolution structure determination, described binding of the pocket domain of the RB1 (retinoblastoma) tumor suppressor protein to an LxCxE motif within E2F that represses the transcriptional activity of E2F. Scott Lowe (Cold Spring Harbor Laboratory, USA) described the involvement of the tumor suppressors RB1 and p19ARF in oncogene-mediated signaling to activate the tumor suppressor protein TP53 (p53), which, in turn, leads to cell-cycle arrest or apoptosis1. This oncogene-signaling pathway via the tumor suppressors was suggested to function as a safety mechanism for tumor surveillance. The conference explored the control of gene transcription by regulators beyond DNA-binding transcription 0168-9525/99/$ – see front matter © 1999 Elsevier Science All rights reserved. PII: S0168-9525(98)01646-1
factors. Marian Carlson (Columbia Univ., USA) described the elegant genetic and biochemical dissection of the functions of the Snf1p kinase (the yeast homologue of the mammalian AMP-activated protein kinase)2. Snf1p phosphorylates the Mig1p repressor inhibiting its function in glucose-induced gene repression. At the same time, Snf1p activates Sip4p, an activator of the same genes. Craig Mizzen (Univ. of Virginia, USA) described the Allis lab’s identification of histone acetyltransferase activity in several transcription co-activators (e.g. Gcn5, TAFII250). Mizzen also presented evidence implicating RSK2, a member of the p90 rsk family of mitogen-activated kinases, in the phosphorylation of histone H3. RSK2 is causally linked to the Coffin–Lowry syndrome (CLS). Cell lines from CLS patients fail to demonstrate H3 phosphorylation in response to mitogen stimulation. The theme of histone modification in transcription control was furthered by the presentations of Michael Grunstein (UCLA), Kevin Struhl (Harvard Univ., USA) and Robert Eisenman (Fred Hutchinson Cancer Research Center, USA). These three presentations implicated histone deacetylases (HDs) in processes of transcriptional repression in yeast and mammalian cells3. Another type of chromatin modifying complexes (ATP-dependent nucleosome remodeling complexes) was illustrated by the presentation of Beverly Emerson (Salk Institute, USA). Emerson described the striking discovery that an EKLF (a erythroid transcription factor) specific co-activator, E-RC1, is potentially a tissuespecific form of the Swi/Snf chromatin remodeling complex4. Another example of the important roles of this family of DNA-dependent ATPases was revealed through the discovery by David Price (Univ. of Iowa, USA) that factor 2, an ATP-dependent RNA polymerase II termination factor, is also a member of the Swi/Snf family of proteins. TIG January 1999, volume 15, No. 1
Jerry L. Workman [email protected] Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. 9
Outlook
MEETING REPORTS
Gene regulation and cancer
FIGURE 1. cDNA microarray analysis
Trends in Genetics
Image from an experiment using a 6000 gene cDNA microarray in which cDNA from human mammary epithelial cells was labeled in green and the breast-carcinoma-derived cell line BT-474 in red (see magnified inset for detail). A large number of differences in cDNA abundance are evident, some of which can be attributed to amplification of the 17q12–21 region in BT-474, which is known to contain the ERBB2 (HER2) oncogene. (Contributed by Charles M. Perou, Dept of Genetics, Stanford University, USA.)
An exciting concept emerging in the conference was that of exploiting specific genetic defects in cancer cells as potential vulnerabilities for therapeutic intervention. Leland Hartwell (Fred Hutchinson Cancer Research Center, USA) described ‘synthetic lethal’ screens in yeast using strains defective in processes similar to those in many cancer cells (e.g. checkpoints for DNA repair) to identify compounds to which the mutant strains are susceptible5. The utility of this approach is evidenced by their finding that groups of related yeast mutants show increased sensitivity to specific anticancer drugs. The next
step will be to identify specific cancers that harbor similar defects and are thus optimum targets for the identified compounds. One approach toward characterizing specific tumors is through the use of microarray technology, which was described by Stephen Friend (Fred Hutchinson Cancer Research Center, USA)6. Indeed, Charles Perou (Stanford Univ., USA) described the use of cDNA microarrays to classify human breast tumors based on altered patterns of gene expression (Fig. 1). For example, many breast cancers overexpress HER2 (ERBB2) a member of the epidermal growth factor family of receptors. HER2 already represents an example of a specific target for cancer treatment. Mark Sliwkowski (Genetech, USA) described the development of Herceptin®, a monoclonal antibody against HER2, which was recently approved by the FDA for treatment of metastatic breast cancer patients whose tumors overexpress HER2. The potential for the development of additional therapeutic approaches was suggested by many of the presentations. These possibilities range from interfering with the anti-apoptotic functions of NF-kB (Albert Baldwin, UNC, USA) and BCL2 (Craig Thompson, Univ. of Chicago, USA), to blocking the function of HIF1, which allows tumor cells to adapt to hypoxia (Gregg Semenza, Johns Hopkins, USA) and inhibition of farnesyl protein transferase, which is required for RAS to anchor to the plasma membrane (Ivan Horak, Janssen Research Foundation, USA). Thus, while this conference illustrated the dramatic progress made over the past decade in understanding pathways regulating gene expression and their relationship to cancer, it also revealed the impact that these advances are bringing to the treatment of cancer.
Further reading 1 Chin, L. et al. (1998) The INK4a/ARF tumor suppressor: one gene – two products – two pathways. Trends Biochem. Sci. 23, 291–296 2 Hardie, D.G. (1998) The AMP-activated/SNF1 protein kinase subfamily: metabolic sensors of the eukaryotic cell? Annu. Rev. Biochem. 67, 821–855 3 Struhl, K. (1998) Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12, 599–606 4 Armstrong, J.A. and Emerson, B.M. (1998) Transcription of chromatin: these are complex times. Curr. Opin. Genet. Dev. 8, 165–172 5 Hartwell, L.H. et al. (1997) Integrating genetic approaches into the discovery of anticancer drugs. Science 7, 1064–1068 6 Schena, M. et al. (1998) Microarrays: biotechnology’s discovery platform for functional genomics. Trends Biotechnol. 16, 301–306
Okazaki fragments in dynamic mutation The recent review of chromosomal fragile sites1 discussed the dynamic mutation mechanism of repeat expansion that gives rise to the ‘rare’ fragile sites, and highlighted evidence that Okazaki fragments have a role to play in the mutation process. Further support for the role of Okazaki fragments in the dynamic mutation of DNA repeats comes from the work of Sarkar et al.2 who demonstrated a similar bimodal (minor/major) amplification of the CTG trinucleotide repeat in E. coli as is seen in the human genetic diseases. The repeat length at which amplification in E. coli alters again coincides with the approximate length of the Okazaki fragment (which is longer in E. coli than in humans). These data are consistent with the proposal (as illustrated in Fig. 2, Ref. 1; and first proposed in Ref. 3) that Okazaki fragments that are anchored by unique DNA flanking shorter repeats facilitate minor expansions, whereas Okazaki fragments that are entirely contained within the longer repeats are subject to major expansions. 1 Sutherland, G.R. et al. (1998) Fragile sites still breaking. Trends Genet. 14, 501–506 2 Sarkar, P.S. et al. (1998) CTG repeats show bimodal amplification in E. coli. Cell 95, 531–540 3 Richards, R.I. and Sutherland, G.R. (1994) Simple repeat DNA is not replicated simply. Nat. Genet. 6, 114–116 *G.R. Sutherland, *E. Baker and §R.I. Richards are at the Centre for Medical Genetics, Department of Cytogenetics and Molecular Genetics, Women’s and Children’s Hospital, Adelaide 5006, and Department of Paediatrics* and Genetics §, University of Adelaide, Adelaide 5000, Australia.
10
TIG January 1999, volume 15, No. 1
Bioinformatics in Siberia
structural properties of whole genomes. Oral presentations were complemented by about 80 posters, detailing a wealth of specialized databases, computer programs and models, attesting to the vitality of the field both in Russia and across the world. We refer the reader to the web page containing links to all the relevant information, including the full program of the meeting and abstracts2. Full proceedings of the conference can be ordered from Nikolay Kolchanov ([email protected]). Finally, a selection of papers will be published in a forthcoming special issue of Bioinformatics. As the meeting unfolded, Russia was sinking deeper into political and economic crisis. The situation for Russian scientists is becoming ever more difficult. Salaries are hardly paid, and in any case, have lost much of their already low value. Payment of grants has often been suspended. Basic experimental materials are scarce, and in some institutes, even telephone and fax lines have been cut off because of the lack of money. In such a
Outlook
problematic context, bioinformatics constitutes an interesting alternative. Indeed, with electricity, a few computers, and access to the web, Russian scientists can face economic and political adversities and pursue their research. The visit to the Institute of Cytology and Genetics in Novosibirsk gave us a striking demonstration that Russian scientists are far from giving up and are courageously looking for every way to do interesting science. To support these efforts, the best we can do is publicize their achievements and, whenever possible, engage in fruitful international collaborations. The results of a number of such collaborations were presented at the conference.
Further reading 1 Ashburner, M. and Goodman, N. (1997) Informatics – genomes and genetic databases. Curr. Opin. Genet. Dev. 7, 750–756 2 Bioinformatics of Genome Regulation and Structure, http://bgrs.bionet.nsc.ru
Gene regulation and cancer Gene Regulation and Cancer: 10th Anniversary Meeting of the American Association of Cancer Research Special Conferences in Cancer Research, The Homestead, Hot Springs, Virginia, USA, 14–18 October 1998. Ten years ago, Phillip Sharp (MIT, USA) and Steven McKnight (UT Southwest Medical Center, USA) organized the first AACR Special Conference in Cancer Research on the subject of ‘Gene Regulation and Cancer’. With the support of a major educational grant from Janssen Pharmaceutica and the Janssen Research Foundation, Sharp, McKnight and Jacqueline Lees (MIT, USA) convened another AACR Special Conference on the same topic. This year’s conference dramatically illustrated the advances of the past decade over a broad front ranging from analysis of protein structure to clinical trials for new therapeutics. An important topic of the conference was the functions of oncogenes and tumor suppressors in cell proliferation and development. For example, Jacqueline Lees (MIT, USA) described the E2F family of transcriptional activators and illustrated, through phenotypic analysis of transgenic mice, that E2F4 (the major E2F form in vivo) plays a crucial role in the terminal differentiation of hemopoietic cell lineages. Nikola Pavletich (Memorial Sloan-Kettering Cancer Center, USA), through high-resolution structure determination, described binding of the pocket domain of the RB1 (retinoblastoma) tumor suppressor protein to an LxCxE motif within E2F that represses the transcriptional activity of E2F. Scott Lowe (Cold Spring Harbor Laboratory, USA) described the involvement of the tumor suppressors RB1 and p19ARF in oncogene-mediated signaling to activate the tumor suppressor protein TP53 (p53), which, in turn, leads to cell-cycle arrest or apoptosis1. This oncogene-signaling pathway via the tumor suppressors was suggested to function as a safety mechanism for tumor surveillance. The conference explored the control of gene transcription by regulators beyond DNA-binding transcription 0168-9525/99/$ – see front matter © 1999 Elsevier Science All rights reserved. PII: S0168-9525(98)01646-1
factors. Marian Carlson (Columbia Univ., USA) described the elegant genetic and biochemical dissection of the functions of the Snf1p kinase (the yeast homologue of the mammalian AMP-activated protein kinase)2. Snf1p phosphorylates the Mig1p repressor inhibiting its function in glucose-induced gene repression. At the same time, Snf1p activates Sip4p, an activator of the same genes. Craig Mizzen (Univ. of Virginia, USA) described the Allis lab’s identification of histone acetyltransferase activity in several transcription co-activators (e.g. Gcn5, TAFII250). Mizzen also presented evidence implicating RSK2, a member of the p90 rsk family of mitogen-activated kinases, in the phosphorylation of histone H3. RSK2 is causally linked to the Coffin–Lowry syndrome (CLS). Cell lines from CLS patients fail to demonstrate H3 phosphorylation in response to mitogen stimulation. The theme of histone modification in transcription control was furthered by the presentations of Michael Grunstein (UCLA), Kevin Struhl (Harvard Univ., USA) and Robert Eisenman (Fred Hutchinson Cancer Research Center, USA). These three presentations implicated histone deacetylases (HDs) in processes of transcriptional repression in yeast and mammalian cells3. Another type of chromatin modifying complexes (ATP-dependent nucleosome remodeling complexes) was illustrated by the presentation of Beverly Emerson (Salk Institute, USA). Emerson described the striking discovery that an EKLF (a erythroid transcription factor) specific co-activator, E-RC1, is potentially a tissuespecific form of the Swi/Snf chromatin remodeling complex4. Another example of the important roles of this family of DNA-dependent ATPases was revealed through the discovery by David Price (Univ. of Iowa, USA) that factor 2, an ATP-dependent RNA polymerase II termination factor, is also a member of the Swi/Snf family of proteins. TIG January 1999, volume 15, No. 1
Jerry L. Workman [email protected] Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. 9
Outlook
MEETING REPORTS
Gene regulation and cancer
FIGURE 1. cDNA microarray analysis
Trends in Genetics
Image from an experiment using a 6000 gene cDNA microarray in which cDNA from human mammary epithelial cells was labeled in green and the breast-carcinoma-derived cell line BT-474 in red (see magnified inset for detail). A large number of differences in cDNA abundance are evident, some of which can be attributed to amplification of the 17q12–21 region in BT-474, which is known to contain the ERBB2 (HER2) oncogene. (Contributed by Charles M. Perou, Dept of Genetics, Stanford University, USA.)
An exciting concept emerging in the conference was that of exploiting specific genetic defects in cancer cells as potential vulnerabilities for therapeutic intervention. Leland Hartwell (Fred Hutchinson Cancer Research Center, USA) described ‘synthetic lethal’ screens in yeast using strains defective in processes similar to those in many cancer cells (e.g. checkpoints for DNA repair) to identify compounds to which the mutant strains are susceptible5. The utility of this approach is evidenced by their finding that groups of related yeast mutants show increased sensitivity to specific anticancer drugs. The next
step will be to identify specific cancers that harbor similar defects and are thus optimum targets for the identified compounds. One approach toward characterizing specific tumors is through the use of microarray technology, which was described by Stephen Friend (Fred Hutchinson Cancer Research Center, USA)6. Indeed, Charles Perou (Stanford Univ., USA) described the use of cDNA microarrays to classify human breast tumors based on altered patterns of gene expression (Fig. 1). For example, many breast cancers overexpress HER2 (ERBB2) a member of the epidermal growth factor family of receptors. HER2 already represents an example of a specific target for cancer treatment. Mark Sliwkowski (Genetech, USA) described the development of Herceptin®, a monoclonal antibody against HER2, which was recently approved by the FDA for treatment of metastatic breast cancer patients whose tumors overexpress HER2. The potential for the development of additional therapeutic approaches was suggested by many of the presentations. These possibilities range from interfering with the anti-apoptotic functions of NF-kB (Albert Baldwin, UNC, USA) and BCL2 (Craig Thompson, Univ. of Chicago, USA), to blocking the function of HIF1, which allows tumor cells to adapt to hypoxia (Gregg Semenza, Johns Hopkins, USA) and inhibition of farnesyl protein transferase, which is required for RAS to anchor to the plasma membrane (Ivan Horak, Janssen Research Foundation, USA). Thus, while this conference illustrated the dramatic progress made over the past decade in understanding pathways regulating gene expression and their relationship to cancer, it also revealed the impact that these advances are bringing to the treatment of cancer.
Further reading 1 Chin, L. et al. (1998) The INK4a/ARF tumor suppressor: one gene – two products – two pathways. Trends Biochem. Sci. 23, 291–296 2 Hardie, D.G. (1998) The AMP-activated/SNF1 protein kinase subfamily: metabolic sensors of the eukaryotic cell? Annu. Rev. Biochem. 67, 821–855 3 Struhl, K. (1998) Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12, 599–606 4 Armstrong, J.A. and Emerson, B.M. (1998) Transcription of chromatin: these are complex times. Curr. Opin. Genet. Dev. 8, 165–172 5 Hartwell, L.H. et al. (1997) Integrating genetic approaches into the discovery of anticancer drugs. Science 7, 1064–1068 6 Schena, M. et al. (1998) Microarrays: biotechnology’s discovery platform for functional genomics. Trends Biotechnol. 16, 301–306
Okazaki fragments in dynamic mutation The recent review of chromosomal fragile sites1 discussed the dynamic mutation mechanism of repeat expansion that gives rise to the ‘rare’ fragile sites, and highlighted evidence that Okazaki fragments have a role to play in the mutation process. Further support for the role of Okazaki fragments in the dynamic mutation of DNA repeats comes from the work of Sarkar et al.2 who demonstrated a similar bimodal (minor/major) amplification of the CTG trinucleotide repeat in E. coli as is seen in the human genetic diseases. The repeat length at which amplification in E. coli alters again coincides with the approximate length of the Okazaki fragment (which is longer in E. coli than in humans). These data are consistent with the proposal (as illustrated in Fig. 2, Ref. 1; and first proposed in Ref. 3) that Okazaki fragments that are anchored by unique DNA flanking shorter repeats facilitate minor expansions, whereas Okazaki fragments that are entirely contained within the longer repeats are subject to major expansions. 1 Sutherland, G.R. et al. (1998) Fragile sites still breaking. Trends Genet. 14, 501–506 2 Sarkar, P.S. et al. (1998) CTG repeats show bimodal amplification in E. coli. Cell 95, 531–540 3 Richards, R.I. and Sutherland, G.R. (1994) Simple repeat DNA is not replicated simply. Nat. Genet. 6, 114–116 *G.R. Sutherland, *E. Baker and §R.I. Richards are at the Centre for Medical Genetics, Department of Cytogenetics and Molecular Genetics, Women’s and Children’s Hospital, Adelaide 5006, and Department of Paediatrics* and Genetics §, University of Adelaide, Adelaide 5000, Australia.
10
TIG January 1999, volume 15, No. 1