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Patent and be damned: the new slogan for human genetics?
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MOLECULAR MEDICINE TODAY, JULY 2000 (VOL. 6)
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Patent and be damned: the new slogan for human genetics? Following the release of the full sequence of chromosome 21 in May 2000, the Human Genome Project (HGP) added further sequence data to its public domain database and completed its ‘working draft’ of the human genome in June. This represents a low coverage sequence of 90% of the euchromatic DNA and will be published in print form in September. ‘By low coverage, we mean that most of the sequence has been covered 3–5 times. Now we have to work towards increasing the coverage, so that the sequence data increases its overall accuracy,’ explains Ian Dunham (Sanger Centre, Cambridge, UK). Dunham also predicts that this year should see the publication of other complete chromosomes, with chromosomes 20 and Y likely to be next, ‘but the sequencing project for all chromosomes will not be completed until the end of 2003,’ he says. The HGP, which began in 1990, has been releasing human genome sequence data into the public domain for five years; the working draft is yet another interim stage in that process. ‘This is the fundamental difference between our sequence and that produced by Celera Genomics (Rockville, MD, USA); as we have unravelled the sequence, the constant release of data into the public domain has enabled scientists worldwide to use and benefit from it. In contrast, it is not yet clear whether Celera may restrict access to its whole genome shotgun sequence or lay claim to the rights of downsteam development work.’ The company has been busy filing provisional patent applications on gene sequences; 6500 such applications were made within the space of one month last autumn. At the time, Craig Venter, President and Chief Scientific Officer at Celera, was heavily criticised for saying publicly that he expected to receive patents on only 100–300 stretches of human genetic material, but then filing thousands of applications. He defended his actions by saying that most of the provisional patents would be dropped and only the most promising genes would go through for the next, more expensive and time-consuming full patent application process. Nevertheless, Celera seems on track to file between 20 000 and 30 000 provisional applications. In Dunham’s opinion, compositional patents – those that have a claim on DNA sequence information alone – could damage the potential for future exploitation of those genes, either by
academic researchers wishing to use them to study disease, or by pharmaceutical companies wanting to develop therapeutic products. ‘The worst case scenario would be hundreds of key genes tied up in patent applications, preventing anyone from using them for anything.’ he says. The position on gene patents has been confused. A joint statement on March 14
2000 by President Clinton and Prime Minister Tony Blair did nothing to help; they proclaimed that ‘to realise the full promise of this research, raw fundamental data on the human genome... should be made freely available to scientists everywhere.’ Later, on April 5, Clinton added that although general information on the human genome sequence
Box 1. Patent success but new controversy for cloning researchers In January, PPL Therapeutics (Edinburgh, UK), together with the Roslin Institute (Edinburgh, UK) and the Geron Corporation (Menlo Park, CA, USA), was granted two patents relating to its cloning technology by the UK Patent Office. A patent application filed in the US is still being considered but could be granted later this year. The patents have broad generic claims to methods of nuclear transfer and of methods for producing cloned, non-human animals, including transgenic cloned animals. Neither of these patents relate to human therapeutic cloning, a research field that is currently outlawed in the most countries. However, in February, a European patent granted to Edinburgh University (Edinburgh, UK) for research to look at the possibility of using cloned cells to treat Parkinson’s disease ran into trouble when a complaint from Greenpeace revealed a serious error in the wording of the patent. Referring only to ‘a method of preparing a transgenic animal’, the term ‘non-human’ was omitted. The patent violates European Union guidelines banning processes that would change the identity of human organisms, which come into effect at the end of July, and is now being challenged by the German and Italian governments. This new storm coincides with the recommendation from the UK Advisory Group on Therapeutic Cloning, led by the Chief Medical Officer for England, Liam Donaldson, that the UK government accepts limited cloning work for the purposes of human therapeutics. Ian Wilmut, (Roslin Institute, Edinburgh, UK), who led the team that cloned Dolly, has spoken out strongly in support of human cloning research. ‘Our experiments with sheep cloning have shown that oocyte cytoplasm contains factors that reprogram a somatic cell nucleus and enable it to develop into a normal embryo. It is clear that embryonic stem (ES) cells obtained from such an embryo would have enormous therapeutic applications, but only human ES cells could be used to develop treatments for human disease,’ he says. However, as an alternative approach to reprogramming nuclei from somatic cells, experiments in mice have shown that ES cells contain factors that allow substantial reprogramming of somatic cells. Whether ES cells are as powerful as oocytes, remains to be seen. ‘There is a lot of basic research ahead in animals to discover which proteins in the oocyte cytoplasm are involved in reprogramming. It may take between five and ten years to fully understand which factors are involved,’ he adds. Although much can be learned from work with human cells in vitro and from animal work in vivo, there will come a point, says Wilmut, where some human embryo work will need to be done. ‘Peripheral stem cells hold a great deal of promise as progenitor cells for cloned human tissue but, before we can develop the technology to reprogram them into required cell types, we need to understand much more about how this process occurs in the embryo.’ There seems to be broad agreement on this point; in April, the Nuffield Council on Bioethics recommended ‘that research involving human embryos be permitted for the purposes of developing tissues to treat diseases, from derived embryonic stem cells and that Schedule 2 of the Human Fertilisation and Embryology Act be amended accordingly’ (for further information, see http://www.nuffieldfoundation.org/ bioethics/publication/stemcell/p_0022221.html).
1357-4310/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved.
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should be freely available, ‘if someone discovers something that has a specific commercial application, they ought to be able to get a patent on it.’ At a National Institutes of Health (NIH) Council of Public Representatives meeting on April 6, Francis Collins, Director of the National Human Genome Research Institute (NHGRI; Bethesda, MD, USA) further clarified the criteria that both the NIH and the Patent and Trademark Office consider satisfy utility claims for gene patents. A patent may be granted for: (1) a gene that codes for a protein that has potential as a pharmaceutical; (2) a gene that is found to be involved in a particular disease, because it could have potential as a useful diagnostic; and (3) a gene that codes for a protein of known function that might be used to create assays used in treatment development. Randy Scott, Chief Executive Officer at Incyte Genomics (Palo Alto, CA, USA), a company that filed patent applications on 1.2 million expressed sequence tags in late 1998, believes that gene patents will go
MOLECULAR MEDICINE TODAY, JULY 2000 (VOL. 6)
ahead, but will not be detrimental to future research. ‘Quite the opposite,’ he says. He points out that gene patents are not new; companies such as Amgen and Genentech made the first applications 20 years ago, for the genes that code, for example, for growth hormone and erythropoietin. ‘History shows that these patents had a positive effect on the amount of research effort put into these areas, both in academia and in the pharmaceutical sector,’ he says. Scott stresses that it is not the possession of gene patents that is important, but what the patent holder does with them. ‘Incyte’s gene patents are licensed non-exclusively and 18 out of ten of the world’s top pharmaceutical companies are able to use genes that we have patented,’ he explains. The companies involved gain access to sequence information about the gene and to research reagents, in return for a commercial fee. ‘We actually charge relatively little for licences,’ says Scott, ‘ but because so many companies are using them, our overall revenue is still substantial.’
Venter told a hearing of the Environment Subcommittee of the US government in April 2000 that Celera intends to licence its patents on a non-exclusive basis, and to only patent genes with proven utility. Scott views this as an entirely reasonable approach. ‘The current rift between scientists at Celera and researchers within the public sequencing project, and the arguments over patenting is troubling, but these disagreements are probably symptomatic of the tremendous changes that the sequence is bringing to research,’ he says. In the past few years, for the first time, genes have been fully sequenced before their biological function has been known. Downstream work is needed to work out what individual genes do, and how useful they will be therapeutically but, says Scott, ‘a commercial enterprise cannot afford to wait and see before deciding whether to patent or not.’ Kathryn Senior Freelance science writer
Bone-marrow analysis predicts breast-cancer recurrence Thousands of lives could be saved if it were possible to detect and eliminate occult metastatic cells before they become a problem. Such occult tumour cells, or micrometastases, are missed by conventional diagnostic procedures, but can be detected by sensitive immunologic or molecular methods. However, there is a clear need to standardize those techniques before they can be routinely used in the clinic. A large study employing a cytokeratin antibody now raises hopes: German scientists have demonstrated that immunostaining of micrometastases in bone marrow can indeed be used to predict metastatic relapse in patients with breast cancer. Long before diagnosis and surgical removal of an epithelial tumour, single carcinoma cells can loosen their adhesion to the neighbouring tumour tissue and disseminate to lymph nodes, blood or distant organs, including bone marrow. After tumour resection, these cells remain in the body of the patient, a disease stage that is called minimal residual disease. Micrometastases are mostly dormant, but eventually may start to proliferate again and produce a tumour at a new site. A good place to look for occult 256
metastatic cells in patients with breast cancer is the bone marrow, because the skeleton is often the first site of relapse. Naturally, these micrometastases carry the characteristics of the epithelial tissue they derive from and can thus be distinguished from haematopoetic or lymphatic cells. The current gold standard to detect occult tumour cells is to immunostain them, using antibodies against cytokeratins, proteins forming part of the inner skeleton of epithelial cells. Unfortunately, not all antibodies used in previous studies have been specific enough, and experiments to establish a relationship between the presence of cytokeratin-positive cells in bone marrow and tumour recurrence have produced controversial results. Therefore, the German group carefully evaluated and validated their technology before they went into clinical trial. Their antibody is directed against cytokeratin heterodimers 8Ð18 and 8Ð19. Stephan Braun at the University of Munich (Munich, Germany), lead author of the study, says, ‘The antibody did not show cross-reactivity in healthy controls and cell lines. It was also more sensitive than other, previously employed cytokeratin antibodies. In addition,
it did not bind to the cytokeratin of skin cells. We were therefore sure that we would be staining micrometastases and not skin-cell contaminations.’ The scientists then conducted a study with 552 patients with breast cancer1. The tumour was completely removed in all patients; the lymph nodes were also dissected. Patients treated with breast-conserving surgery received radiation therapy. All of the node-positive patients and a few of the node-negative patients received adjuvant chemo- or hormone therapy. Before primary surgery, bone-marrow probes were taken by needle aspiration and evaluated for the presence of micrometastases. The researchers found these occult tumour cells in 36% of all patients. The incidence of micrometastases was similar in patients with lymph-node metastasis and those without it. After a median follow-up of 38 months, the presence of micrometastases in bone marrow proved to be an independent risk factor for tumour recurrence and cancer-related death, next to lymph node metastasis and the presence of oestrogen receptors. Bjørn Naume at the Oncology Department of the Norwegian Radiation Hospital (Oslo,
1357-4310/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved.
MOLECULAR MEDICINE TODAY, JULY 2000 (VOL. 6)
e
w
s
Patent and be damned: the new slogan for human genetics? Following the release of the full sequence of chromosome 21 in May 2000, the Human Genome Project (HGP) added further sequence data to its public domain database and completed its ‘working draft’ of the human genome in June. This represents a low coverage sequence of 90% of the euchromatic DNA and will be published in print form in September. ‘By low coverage, we mean that most of the sequence has been covered 3–5 times. Now we have to work towards increasing the coverage, so that the sequence data increases its overall accuracy,’ explains Ian Dunham (Sanger Centre, Cambridge, UK). Dunham also predicts that this year should see the publication of other complete chromosomes, with chromosomes 20 and Y likely to be next, ‘but the sequencing project for all chromosomes will not be completed until the end of 2003,’ he says. The HGP, which began in 1990, has been releasing human genome sequence data into the public domain for five years; the working draft is yet another interim stage in that process. ‘This is the fundamental difference between our sequence and that produced by Celera Genomics (Rockville, MD, USA); as we have unravelled the sequence, the constant release of data into the public domain has enabled scientists worldwide to use and benefit from it. In contrast, it is not yet clear whether Celera may restrict access to its whole genome shotgun sequence or lay claim to the rights of downsteam development work.’ The company has been busy filing provisional patent applications on gene sequences; 6500 such applications were made within the space of one month last autumn. At the time, Craig Venter, President and Chief Scientific Officer at Celera, was heavily criticised for saying publicly that he expected to receive patents on only 100–300 stretches of human genetic material, but then filing thousands of applications. He defended his actions by saying that most of the provisional patents would be dropped and only the most promising genes would go through for the next, more expensive and time-consuming full patent application process. Nevertheless, Celera seems on track to file between 20 000 and 30 000 provisional applications. In Dunham’s opinion, compositional patents – those that have a claim on DNA sequence information alone – could damage the potential for future exploitation of those genes, either by
academic researchers wishing to use them to study disease, or by pharmaceutical companies wanting to develop therapeutic products. ‘The worst case scenario would be hundreds of key genes tied up in patent applications, preventing anyone from using them for anything.’ he says. The position on gene patents has been confused. A joint statement on March 14
2000 by President Clinton and Prime Minister Tony Blair did nothing to help; they proclaimed that ‘to realise the full promise of this research, raw fundamental data on the human genome... should be made freely available to scientists everywhere.’ Later, on April 5, Clinton added that although general information on the human genome sequence
Box 1. Patent success but new controversy for cloning researchers In January, PPL Therapeutics (Edinburgh, UK), together with the Roslin Institute (Edinburgh, UK) and the Geron Corporation (Menlo Park, CA, USA), was granted two patents relating to its cloning technology by the UK Patent Office. A patent application filed in the US is still being considered but could be granted later this year. The patents have broad generic claims to methods of nuclear transfer and of methods for producing cloned, non-human animals, including transgenic cloned animals. Neither of these patents relate to human therapeutic cloning, a research field that is currently outlawed in the most countries. However, in February, a European patent granted to Edinburgh University (Edinburgh, UK) for research to look at the possibility of using cloned cells to treat Parkinson’s disease ran into trouble when a complaint from Greenpeace revealed a serious error in the wording of the patent. Referring only to ‘a method of preparing a transgenic animal’, the term ‘non-human’ was omitted. The patent violates European Union guidelines banning processes that would change the identity of human organisms, which come into effect at the end of July, and is now being challenged by the German and Italian governments. This new storm coincides with the recommendation from the UK Advisory Group on Therapeutic Cloning, led by the Chief Medical Officer for England, Liam Donaldson, that the UK government accepts limited cloning work for the purposes of human therapeutics. Ian Wilmut, (Roslin Institute, Edinburgh, UK), who led the team that cloned Dolly, has spoken out strongly in support of human cloning research. ‘Our experiments with sheep cloning have shown that oocyte cytoplasm contains factors that reprogram a somatic cell nucleus and enable it to develop into a normal embryo. It is clear that embryonic stem (ES) cells obtained from such an embryo would have enormous therapeutic applications, but only human ES cells could be used to develop treatments for human disease,’ he says. However, as an alternative approach to reprogramming nuclei from somatic cells, experiments in mice have shown that ES cells contain factors that allow substantial reprogramming of somatic cells. Whether ES cells are as powerful as oocytes, remains to be seen. ‘There is a lot of basic research ahead in animals to discover which proteins in the oocyte cytoplasm are involved in reprogramming. It may take between five and ten years to fully understand which factors are involved,’ he adds. Although much can be learned from work with human cells in vitro and from animal work in vivo, there will come a point, says Wilmut, where some human embryo work will need to be done. ‘Peripheral stem cells hold a great deal of promise as progenitor cells for cloned human tissue but, before we can develop the technology to reprogram them into required cell types, we need to understand much more about how this process occurs in the embryo.’ There seems to be broad agreement on this point; in April, the Nuffield Council on Bioethics recommended ‘that research involving human embryos be permitted for the purposes of developing tissues to treat diseases, from derived embryonic stem cells and that Schedule 2 of the Human Fertilisation and Embryology Act be amended accordingly’ (for further information, see http://www.nuffieldfoundation.org/ bioethics/publication/stemcell/p_0022221.html).
1357-4310/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved.
255
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e
w
s
should be freely available, ‘if someone discovers something that has a specific commercial application, they ought to be able to get a patent on it.’ At a National Institutes of Health (NIH) Council of Public Representatives meeting on April 6, Francis Collins, Director of the National Human Genome Research Institute (NHGRI; Bethesda, MD, USA) further clarified the criteria that both the NIH and the Patent and Trademark Office consider satisfy utility claims for gene patents. A patent may be granted for: (1) a gene that codes for a protein that has potential as a pharmaceutical; (2) a gene that is found to be involved in a particular disease, because it could have potential as a useful diagnostic; and (3) a gene that codes for a protein of known function that might be used to create assays used in treatment development. Randy Scott, Chief Executive Officer at Incyte Genomics (Palo Alto, CA, USA), a company that filed patent applications on 1.2 million expressed sequence tags in late 1998, believes that gene patents will go
MOLECULAR MEDICINE TODAY, JULY 2000 (VOL. 6)
ahead, but will not be detrimental to future research. ‘Quite the opposite,’ he says. He points out that gene patents are not new; companies such as Amgen and Genentech made the first applications 20 years ago, for the genes that code, for example, for growth hormone and erythropoietin. ‘History shows that these patents had a positive effect on the amount of research effort put into these areas, both in academia and in the pharmaceutical sector,’ he says. Scott stresses that it is not the possession of gene patents that is important, but what the patent holder does with them. ‘Incyte’s gene patents are licensed non-exclusively and 18 out of ten of the world’s top pharmaceutical companies are able to use genes that we have patented,’ he explains. The companies involved gain access to sequence information about the gene and to research reagents, in return for a commercial fee. ‘We actually charge relatively little for licences,’ says Scott, ‘ but because so many companies are using them, our overall revenue is still substantial.’
Venter told a hearing of the Environment Subcommittee of the US government in April 2000 that Celera intends to licence its patents on a non-exclusive basis, and to only patent genes with proven utility. Scott views this as an entirely reasonable approach. ‘The current rift between scientists at Celera and researchers within the public sequencing project, and the arguments over patenting is troubling, but these disagreements are probably symptomatic of the tremendous changes that the sequence is bringing to research,’ he says. In the past few years, for the first time, genes have been fully sequenced before their biological function has been known. Downstream work is needed to work out what individual genes do, and how useful they will be therapeutically but, says Scott, ‘a commercial enterprise cannot afford to wait and see before deciding whether to patent or not.’ Kathryn Senior Freelance science writer
Bone-marrow analysis predicts breast-cancer recurrence Thousands of lives could be saved if it were possible to detect and eliminate occult metastatic cells before they become a problem. Such occult tumour cells, or micrometastases, are missed by conventional diagnostic procedures, but can be detected by sensitive immunologic or molecular methods. However, there is a clear need to standardize those techniques before they can be routinely used in the clinic. A large study employing a cytokeratin antibody now raises hopes: German scientists have demonstrated that immunostaining of micrometastases in bone marrow can indeed be used to predict metastatic relapse in patients with breast cancer. Long before diagnosis and surgical removal of an epithelial tumour, single carcinoma cells can loosen their adhesion to the neighbouring tumour tissue and disseminate to lymph nodes, blood or distant organs, including bone marrow. After tumour resection, these cells remain in the body of the patient, a disease stage that is called minimal residual disease. Micrometastases are mostly dormant, but eventually may start to proliferate again and produce a tumour at a new site. A good place to look for occult 256
metastatic cells in patients with breast cancer is the bone marrow, because the skeleton is often the first site of relapse. Naturally, these micrometastases carry the characteristics of the epithelial tissue they derive from and can thus be distinguished from haematopoetic or lymphatic cells. The current gold standard to detect occult tumour cells is to immunostain them, using antibodies against cytokeratins, proteins forming part of the inner skeleton of epithelial cells. Unfortunately, not all antibodies used in previous studies have been specific enough, and experiments to establish a relationship between the presence of cytokeratin-positive cells in bone marrow and tumour recurrence have produced controversial results. Therefore, the German group carefully evaluated and validated their technology before they went into clinical trial. Their antibody is directed against cytokeratin heterodimers 8Ð18 and 8Ð19. Stephan Braun at the University of Munich (Munich, Germany), lead author of the study, says, ‘The antibody did not show cross-reactivity in healthy controls and cell lines. It was also more sensitive than other, previously employed cytokeratin antibodies. In addition,
it did not bind to the cytokeratin of skin cells. We were therefore sure that we would be staining micrometastases and not skin-cell contaminations.’ The scientists then conducted a study with 552 patients with breast cancer1. The tumour was completely removed in all patients; the lymph nodes were also dissected. Patients treated with breast-conserving surgery received radiation therapy. All of the node-positive patients and a few of the node-negative patients received adjuvant chemo- or hormone therapy. Before primary surgery, bone-marrow probes were taken by needle aspiration and evaluated for the presence of micrometastases. The researchers found these occult tumour cells in 36% of all patients. The incidence of micrometastases was similar in patients with lymph-node metastasis and those without it. After a median follow-up of 38 months, the presence of micrometastases in bone marrow proved to be an independent risk factor for tumour recurrence and cancer-related death, next to lymph node metastasis and the presence of oestrogen receptors. Bjørn Naume at the Oncology Department of the Norwegian Radiation Hospital (Oslo,
1357-4310/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved.