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Genomics and drug discovery
Genomics and drug discovery William A. Haseltine, PhD Rockville, Maryland Genomics, the systematic study of all the genes of an organism, offers a new and much-needed source of systematic productivity for the pharmaceutical industry. The isolation of the majority of human genes in their most useful form is leading to the creation of new drugs based on human proteins, antibodies, peptides, and genes. Human Genome Sciences, Inc, was the first company to use the systematic, genomics approach to discovering drugs, and we have placed 4 of these in clinical trials. Two are described: repifermin (keratinocyte growth factor–2, KGF-2) for wound healing and treatment of mucositis caused by cancer therapy, and B lymphocyte stimulator (BLyS) for stimulation of the immune system. An anti-BLyS antibody drug is in advanced preclinical development for treatment of autoimmune diseases. (J Am Acad Dermatol 2001;45:473-5.)
T
he pharmaceutical industry is in a productivity crisis that has been understood for at least 10 years and is starting to attract widespread attention. The return on the capital that large pharmaceutical companies are investing in drug discovery is only about 25% of what it needs to be to keep investors happy. Double-digit growth is a requirement when spending the sums the major players put into research, typically $2 billion to $4 billion a year. Big pharma needs to boost its productivity at least 4fold. One of the consequences of this squeeze has been an industry-wide consolidation. However, despite the wave of mergers, productivity in absolute terms has been falling, and productivity per dollar has been falling even faster. Genomics, the systematic study of all of an organism’s genes, represents a highly efficient way to discover new drugs that are relatively easily brought to market. As such, it is clear that genomics will play a crucial role in the development of drugs to treat a wide range of conditions. Abnormalities in genes or gene activity underlie most diseases. Knowledge about the functions performed by human genes therefore promises to lead to many-fold improvements in the efficiency of drug development. The result will be a wide variety of new therapies for conditions that are not well treated by current therapies.
From Human Genome Sciences, Inc. Reprint requests: William A. Haseltine, PhD, Human Genome Sciences, Inc, 9410 Key West Ave, Rockville, MD 20850-3338. Published online July 18, 2001. Copyright © 2001 by the American Academy of Dermatology, Inc. 0190-9622/2001/$35.00 + 0 16/1/117383 doi:10.1067/mjd.2001.117383
The approach that has proven most productive from a medical perspective is not sequencing of the whole human genome. That endeavor is valuable for what it reveals about human variation, and it will ultimately provide insights into human evolution. But the most practically rewarding approach to making use of human genes has been to isolate them in the form in which they are used in the body, such as messenger RNA. Genes isolated in this form have their noncoding sequences (introns) already removed by the cell, so the messenger RNA can be used relatively easily to manufacture the corresponding human protein. Its properties and effects can then be investigated. Moreover, isolation of the messenger RNA form of a gene from a particular type of cell confirms that the gene is in use in that cell because cells produce no messenger RNA from genes they are not using. This approach has led to the initial identification of thousands of human genes and provided pointers to their therapeutic application. In contrast, it is difficult to identify unknown genes in chromosomal sequence data unless they resemble known genes, a point made forcibly by the authors of the recent article describing the sequence of chromosome 22.1 Many genes with medical potential—primarily those involved in intercellular signaling—in fact do not have any close resemblance to genes discovered in the fruit fly or in Caenorhabditis elegans and so would not be recognized in chromosomal sequence. Using genes for drug discovery Many human genes and proteins have good potential for use themselves as drugs. Fully human monoclonal antibodies targeting human proteins are also proving to be therapeutically valuable. In many 473
474 Haseltine
cases, regulatory approval may be easier to obtain for such biopharmaceuticals than for small-molecule drugs, currently the dominant class of therapeutics. Biopharmaceuticals are generally less susceptible to toxicities resulting from drug interactions than small molecules, and they require less medicinal chemistry development, since they are naturally compatible with the body. Human Genome Sciences, Inc (HGS) has analyzed messenger RNAs from about 1000 types of human organs, tissues, and cells, in healthy and diseased states, from every developmental stage. The wide range of tissue samples represented ensures that even rarely used genes are included. As early as mid-1995, we estimated that the HGS gene collection included partial- or full-length sequences from more than 95% of all human genes. It includes at least one messenger RNA sequence capable of producing a complete functional protein for the great majority of all human genes. Over the past several years we have developed systematic methods to identify those genes that may be valuable in the creation of new biopharmaceutical drugs, as well as conventional small-molecule drugs. Drugs that consist of human genes, proteins, and antibodies harness the inborn capacity to create an adult body from a single fertilized egg, as well as the ability to maintain and repair that body for decades. I call this new approach to treatment regenerative medicine and have established an electronic journal, E-Biomed: The Journal of Regenerative Medicine, to foster development of this field (http://www.liebert pub.com/EBI/default1.asp). To date, our company has focused the greater part of its efforts on studying signaling molecules, a class that we believe will be of great importance in medicine. Failure of signals that control growth, for example, causes dwarfism at one extreme and gigantism at the other. Failure of signals that control the growth and division of individual cells results in cancer. Psychiatric and muscular disorders are caused by signaling abnormalities in the nervous system. It is possible to identify messenger RNAs that encode signaling proteins because a protein destined to travel to the cell surface must have at one end a special sequence of amino acids that can dissolve in the membrane. Computers can be programmed to recognize the RNA corresponding to signal sequences. To date, we have discovered approximately 10,000 such genes. Comparisons of the genes for these molecules with known genes in public databases indicate that about 90% of them have not been previously reported. HGS has developed novel high-throughput methods suitable for production of small quantities of
J AM ACAD DERMATOL SEPTEMBER 2001
thousands of human proteins simultaneously. The gene for each protein is cloned into a mammalian expression vector, which is introduced into cell cultures. The proteins harvested from these cell cultures are used in tests of activity on cells in culture. We have also developed automated methods to discover the function of the individual proteins. For the first time it is now possible to study the effects of thousands of new proteins on human cells simultaneously, including which genes are activated by each protein. We have measured the effects of thousands of human proteins on more than 150 different cell types. A single experiment may involve analysis of the results of 10,000 human proteins acting on cells of a specific type, measuring 200 parameters per cell at 4 different times. Each day, hundreds of thousands, sometimes millions, of new biologic data bits are created. Fortunately, advances in computer software and hardware have matched our needs. Our approach has been to build an intranet for scientists to use. For example, we searched for a novel immune-cell differentiation signal that induces 10% or more of the cell-cycle genes in a particular T-cell line by 5fold or more. Just 4 genes came up. It would be typical for us to subject interesting genes such as these to several hundred tests. We are considering developing as a drug a T-cell–stimulating protein identified this way. Specificity and effectiveness Once a reproducible effect is documented, larger amounts of the protein—1 to 2 mg—are purified. The activity of the protein is then assessed both on the target cell and on a wide variety of different types of cells. We select for development only those that are active on the cell type of interest and no other cell types. Repifermin (keratinocyte growth factor–2, KGF-2) is a human growth factor identified through the HGS genomics program that causes some injured tissues to grow rapidly.2 Although several proteins had similar effects on cells, only repifermin had the requisite specificity. Repifermin affects the healing of wounds by both direct and indirect mechanisms. Repifermin has direct effects on epithelial cells and direct chemotactic effects on tissue remodeling. Repifermin also acts indirectly in tissue remodeling by increasing expression of other growth factors such as platelet-derived growth factor, transforming growth factors, and fibroblast growth factors, which have roles in tissue repair and regeneration. These direct and indirect mechanisms of action are thought to explain how repifermin contributes early in and throughout the wound healing process.
J AM ACAD DERMATOL VOLUME 45, NUMBER 3
A phase 2a clinical trial established that, applied to the skin, repifermin accelerates healing of venous ulcers. It may also heal diabetic ulcers and bed sores. Given by injection, it may heal wounds to the mucosal tissue that lines the gastrointestinal tract. This drug also has the potential to heal injury to these tissues induced by radiation, cancer treatment, or inflammatory bowel disease. Repifermin is currently being tested in the clinic for some of these uses. GlaxoSmithKline will co-develop repifermin jointly with HGS. Another signaling protein being developed by HGS is B lymphoctye stimulator (BLyS). This growth factor stimulates the proliferation in the blood of B cells, which produce antibodies. Research had sought such a factor for many years; genomics identified it within months of the start of our search. There are many reasons people might benefit from more antibodies: they might be fighting an antibiotic-resistant infection, have AIDS, or be recovering from organ transplantation or chemotherapy. Some patients recovering from chemotherapy do not regain their original level of immunity for 4 or 5 years. In addition, antibody production declines with age, so some older patients benefit from treatment with immunoglobulins. When we tested BLyS in animals,3 we found it could increase the concentration of immunoglobulins A and G by 4- to 8-fold over a 4- to 5-day period, even though it is a human protein and the test subjects were mice and rats. BLyS also stimulates specific immunity if coadministered with the antigen, suggesting a possible role in vaccines. We are preparing to test BLyS in several different diseases and have now started a clinical trial with patients suffering from common variable immunodeficiency. Going
Haseltine 475
from the first publication on BLyS to approval for a clinical trial took only about a year. We know the receptor for BLyS is found only on B cells. That suggests another possible use of BLyS. We have conjugated it with radioiodine and hope to use this form to treat patients with B-cell tumors because the radiation would be delivered almost exclusively to B cells. We are also very interested in antibodies to BLyS. We are working with the leading companies making fully human antibodies. Antibodies against BLyS have potential as therapies for automimmune diseases in which patients appear to have too much BLyS, such as lupus and rheumatoid arthritis. These two examples illustrate the great potential of genomics to help solve the pharmaceutical industry’s productivity crisis. There are many other biopharmaceuticals in development at HGS and at other companies that have recognized the power of this approach, and they are likely to lead to rapid progress in regenerative medicine. Small-molecule drugs are also being developed through the use of targets identified by genomics. When considered along with progress in other areas, such as stem cells and engineered biomaterials, the outlook appears bright for advances against many conditions that are currently not well treated. REFERENCES 1. Dunham I, Shimizu M, Row BA, Chissoe S, Hunt AR, Collins JE, et al. The DNA sequence of human chromosome 22. Nature 1999; 402:489-95. 2. Jimenez PA, Rampy MA. Keratinocyte growth factor-2 accelerates wound healing in incisional wounds. J Surg Res 1999;81: 238-42. 3. Moore PA, Belvedere O, Orr A, Pieri K, LaFleur DW, Feng P, et al. BLyS: member of the tumor necrosis factor family and B lymphocyte stimulator. Science 1999;285:260-3.
T
he pharmaceutical industry is in a productivity crisis that has been understood for at least 10 years and is starting to attract widespread attention. The return on the capital that large pharmaceutical companies are investing in drug discovery is only about 25% of what it needs to be to keep investors happy. Double-digit growth is a requirement when spending the sums the major players put into research, typically $2 billion to $4 billion a year. Big pharma needs to boost its productivity at least 4fold. One of the consequences of this squeeze has been an industry-wide consolidation. However, despite the wave of mergers, productivity in absolute terms has been falling, and productivity per dollar has been falling even faster. Genomics, the systematic study of all of an organism’s genes, represents a highly efficient way to discover new drugs that are relatively easily brought to market. As such, it is clear that genomics will play a crucial role in the development of drugs to treat a wide range of conditions. Abnormalities in genes or gene activity underlie most diseases. Knowledge about the functions performed by human genes therefore promises to lead to many-fold improvements in the efficiency of drug development. The result will be a wide variety of new therapies for conditions that are not well treated by current therapies.
From Human Genome Sciences, Inc. Reprint requests: William A. Haseltine, PhD, Human Genome Sciences, Inc, 9410 Key West Ave, Rockville, MD 20850-3338. Published online July 18, 2001. Copyright © 2001 by the American Academy of Dermatology, Inc. 0190-9622/2001/$35.00 + 0 16/1/117383 doi:10.1067/mjd.2001.117383
The approach that has proven most productive from a medical perspective is not sequencing of the whole human genome. That endeavor is valuable for what it reveals about human variation, and it will ultimately provide insights into human evolution. But the most practically rewarding approach to making use of human genes has been to isolate them in the form in which they are used in the body, such as messenger RNA. Genes isolated in this form have their noncoding sequences (introns) already removed by the cell, so the messenger RNA can be used relatively easily to manufacture the corresponding human protein. Its properties and effects can then be investigated. Moreover, isolation of the messenger RNA form of a gene from a particular type of cell confirms that the gene is in use in that cell because cells produce no messenger RNA from genes they are not using. This approach has led to the initial identification of thousands of human genes and provided pointers to their therapeutic application. In contrast, it is difficult to identify unknown genes in chromosomal sequence data unless they resemble known genes, a point made forcibly by the authors of the recent article describing the sequence of chromosome 22.1 Many genes with medical potential—primarily those involved in intercellular signaling—in fact do not have any close resemblance to genes discovered in the fruit fly or in Caenorhabditis elegans and so would not be recognized in chromosomal sequence. Using genes for drug discovery Many human genes and proteins have good potential for use themselves as drugs. Fully human monoclonal antibodies targeting human proteins are also proving to be therapeutically valuable. In many 473
474 Haseltine
cases, regulatory approval may be easier to obtain for such biopharmaceuticals than for small-molecule drugs, currently the dominant class of therapeutics. Biopharmaceuticals are generally less susceptible to toxicities resulting from drug interactions than small molecules, and they require less medicinal chemistry development, since they are naturally compatible with the body. Human Genome Sciences, Inc (HGS) has analyzed messenger RNAs from about 1000 types of human organs, tissues, and cells, in healthy and diseased states, from every developmental stage. The wide range of tissue samples represented ensures that even rarely used genes are included. As early as mid-1995, we estimated that the HGS gene collection included partial- or full-length sequences from more than 95% of all human genes. It includes at least one messenger RNA sequence capable of producing a complete functional protein for the great majority of all human genes. Over the past several years we have developed systematic methods to identify those genes that may be valuable in the creation of new biopharmaceutical drugs, as well as conventional small-molecule drugs. Drugs that consist of human genes, proteins, and antibodies harness the inborn capacity to create an adult body from a single fertilized egg, as well as the ability to maintain and repair that body for decades. I call this new approach to treatment regenerative medicine and have established an electronic journal, E-Biomed: The Journal of Regenerative Medicine, to foster development of this field (http://www.liebert pub.com/EBI/default1.asp). To date, our company has focused the greater part of its efforts on studying signaling molecules, a class that we believe will be of great importance in medicine. Failure of signals that control growth, for example, causes dwarfism at one extreme and gigantism at the other. Failure of signals that control the growth and division of individual cells results in cancer. Psychiatric and muscular disorders are caused by signaling abnormalities in the nervous system. It is possible to identify messenger RNAs that encode signaling proteins because a protein destined to travel to the cell surface must have at one end a special sequence of amino acids that can dissolve in the membrane. Computers can be programmed to recognize the RNA corresponding to signal sequences. To date, we have discovered approximately 10,000 such genes. Comparisons of the genes for these molecules with known genes in public databases indicate that about 90% of them have not been previously reported. HGS has developed novel high-throughput methods suitable for production of small quantities of
J AM ACAD DERMATOL SEPTEMBER 2001
thousands of human proteins simultaneously. The gene for each protein is cloned into a mammalian expression vector, which is introduced into cell cultures. The proteins harvested from these cell cultures are used in tests of activity on cells in culture. We have also developed automated methods to discover the function of the individual proteins. For the first time it is now possible to study the effects of thousands of new proteins on human cells simultaneously, including which genes are activated by each protein. We have measured the effects of thousands of human proteins on more than 150 different cell types. A single experiment may involve analysis of the results of 10,000 human proteins acting on cells of a specific type, measuring 200 parameters per cell at 4 different times. Each day, hundreds of thousands, sometimes millions, of new biologic data bits are created. Fortunately, advances in computer software and hardware have matched our needs. Our approach has been to build an intranet for scientists to use. For example, we searched for a novel immune-cell differentiation signal that induces 10% or more of the cell-cycle genes in a particular T-cell line by 5fold or more. Just 4 genes came up. It would be typical for us to subject interesting genes such as these to several hundred tests. We are considering developing as a drug a T-cell–stimulating protein identified this way. Specificity and effectiveness Once a reproducible effect is documented, larger amounts of the protein—1 to 2 mg—are purified. The activity of the protein is then assessed both on the target cell and on a wide variety of different types of cells. We select for development only those that are active on the cell type of interest and no other cell types. Repifermin (keratinocyte growth factor–2, KGF-2) is a human growth factor identified through the HGS genomics program that causes some injured tissues to grow rapidly.2 Although several proteins had similar effects on cells, only repifermin had the requisite specificity. Repifermin affects the healing of wounds by both direct and indirect mechanisms. Repifermin has direct effects on epithelial cells and direct chemotactic effects on tissue remodeling. Repifermin also acts indirectly in tissue remodeling by increasing expression of other growth factors such as platelet-derived growth factor, transforming growth factors, and fibroblast growth factors, which have roles in tissue repair and regeneration. These direct and indirect mechanisms of action are thought to explain how repifermin contributes early in and throughout the wound healing process.
J AM ACAD DERMATOL VOLUME 45, NUMBER 3
A phase 2a clinical trial established that, applied to the skin, repifermin accelerates healing of venous ulcers. It may also heal diabetic ulcers and bed sores. Given by injection, it may heal wounds to the mucosal tissue that lines the gastrointestinal tract. This drug also has the potential to heal injury to these tissues induced by radiation, cancer treatment, or inflammatory bowel disease. Repifermin is currently being tested in the clinic for some of these uses. GlaxoSmithKline will co-develop repifermin jointly with HGS. Another signaling protein being developed by HGS is B lymphoctye stimulator (BLyS). This growth factor stimulates the proliferation in the blood of B cells, which produce antibodies. Research had sought such a factor for many years; genomics identified it within months of the start of our search. There are many reasons people might benefit from more antibodies: they might be fighting an antibiotic-resistant infection, have AIDS, or be recovering from organ transplantation or chemotherapy. Some patients recovering from chemotherapy do not regain their original level of immunity for 4 or 5 years. In addition, antibody production declines with age, so some older patients benefit from treatment with immunoglobulins. When we tested BLyS in animals,3 we found it could increase the concentration of immunoglobulins A and G by 4- to 8-fold over a 4- to 5-day period, even though it is a human protein and the test subjects were mice and rats. BLyS also stimulates specific immunity if coadministered with the antigen, suggesting a possible role in vaccines. We are preparing to test BLyS in several different diseases and have now started a clinical trial with patients suffering from common variable immunodeficiency. Going
Haseltine 475
from the first publication on BLyS to approval for a clinical trial took only about a year. We know the receptor for BLyS is found only on B cells. That suggests another possible use of BLyS. We have conjugated it with radioiodine and hope to use this form to treat patients with B-cell tumors because the radiation would be delivered almost exclusively to B cells. We are also very interested in antibodies to BLyS. We are working with the leading companies making fully human antibodies. Antibodies against BLyS have potential as therapies for automimmune diseases in which patients appear to have too much BLyS, such as lupus and rheumatoid arthritis. These two examples illustrate the great potential of genomics to help solve the pharmaceutical industry’s productivity crisis. There are many other biopharmaceuticals in development at HGS and at other companies that have recognized the power of this approach, and they are likely to lead to rapid progress in regenerative medicine. Small-molecule drugs are also being developed through the use of targets identified by genomics. When considered along with progress in other areas, such as stem cells and engineered biomaterials, the outlook appears bright for advances against many conditions that are currently not well treated. REFERENCES 1. Dunham I, Shimizu M, Row BA, Chissoe S, Hunt AR, Collins JE, et al. The DNA sequence of human chromosome 22. Nature 1999; 402:489-95. 2. Jimenez PA, Rampy MA. Keratinocyte growth factor-2 accelerates wound healing in incisional wounds. J Surg Res 1999;81: 238-42. 3. Moore PA, Belvedere O, Orr A, Pieri K, LaFleur DW, Feng P, et al. BLyS: member of the tumor necrosis factor family and B lymphocyte stimulator. Science 1999;285:260-3.