WO1999037817A1 - Gene expression methods for screening compounds - Google Patents
Gene expression methods for screening compounds Download PDFInfo
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- WO1999037817A1 WO1999037817A1 PCT/US1999/001552 US9901552W WO9937817A1 WO 1999037817 A1 WO1999037817 A1 WO 1999037817A1 US 9901552 W US9901552 W US 9901552W WO 9937817 A1 WO9937817 A1 WO 9937817A1
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
- C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
Definitions
- Microarrays of synthetic oligonucleotides or cDNAs are useful in evaluating differential gene expression.
- Schena et al. (Science 270: 467- 470 (1995) disclosed the quantitative monitoring of gene expression patterns in response to transgenes using a complementary DNA microarray.
- Shena et al. (Proc. Natl. Acad. Sci. U.S.A. 93(20): 10614-10619 (1996)) used microassays containing human cDNAs of unknown sequence to quantitatively monitor differential gene expression patterns under given experimental conditions.
- De Risi et al. (Nat. Genet. 14(4): 457-460(1996)) used a cDNA microarray to analyze gene expression patterns in human cancer.
- Heller et al. (Proc. Natl. Acad. Sci. U.S.A. 94(6) :2150-2155 (1997)) disclosed the use of cDNA microarray technology to monitor gene expression in inflammation.
- Other methods for screening include a method for detecting and isolating differentially expressed mRNAs using first oligonucleotide primers for reverse transcription of mRNAs and both the first oligonucleotide primers and second oligonucleotide primers for amplification of the resultant cDNAs (U.S. 5,580,726).
- Rosenberg et al. PCT Publication WO 95/21944
- Lee et al. Cell Biology 92:8303-8307 (1995) 2 disclosed the use of comparative expressed -sequence -tag analysis to identify about 600 differentially expressed in RNAs in untreated and nerve growth factor-treated PC 12 cells.
- Further screening methods include such examples as that of Nilsson et al. (PCT Publication WO 93/07290) who disclosed an in vitro method of evaluating the antagonistic vs agonistic effects of a receptor-binding substance on selected types of cells containing endogenous intracellular hormone receptors by analyzing cellular response to the receptor-binding substance based on the level of expression of the protein product made by a gene regulated by the hormone-receptor interaction.
- WO 96/41013 disclosed a method for identifying a receptor agonist or antagonist using mutant versions of intracellular receptors such as the estrogen (ER), androgen (AR), progesterone (PR), and glucocorticoid (GR) receptors.
- One aspect of the invention is a method for grouping test compounds into classes, the method comprising:
- test compound (e) comparing the GEF for each test compound (d), wherein the test compounds are grouped into at least two classes based on differences in their GEFs.
- test compounds in each class may be further tested for a representative activity or an activity of interest in vivo.
- the at least two gene-cell combinations may, for example, comprise at least two different genes, at least two different cell types, or combinations thereof.
- a gene or genes in the gene-cell combinations may comprise an endogenous gene under control of its native promoter, a heterologous gene under control of a heterologous promoter, an internal negative control gene, wherein an effect on the mRNA level of the negative control gene in response to the test compound is indicative of a toxic effect of the test compound, or an internal negative control gene, wherein the effect on the mRNA level of the negative control gene in response to the test compound is indicative of a non-specific effect of the test compound.
- RNA may comprise PCR amplification using oligonucleotide primers specific for each gene.
- the RNA is optionally reverse transcribed into cDNA.
- the screening comprises hybridization of nucleic acid sequences specific for each gene to the RNA or cDNA of the exposed cell cultures.
- the level of the mRNA of at least one gene in the at least two gene-cell combinations is quantitated.
- combinations of two or more test compounds can be administered to the cell cultures to generate a GEF for the combination.
- a further aspect of the invention is a method of identifying one or more genes for use in a gene-cell combination for grouping test compounds into classes, the method comprising:
- RNA of (c) comparing the RNA of (b) to RNA from host cells in vivo or a control host cell culture not exposed to the first reference compound; wherein at least one gene having an mRNA level affected in response to the first reference compound is identified as a gene for use in a gene-cell combination for grouping test compounds into classes.
- the RNA of (c) may be compared to RNA from host cells in vivo or a control host cell culture, wherein the host cells in vivo or a control host cell culture have or has been exposed to a second reference compound, whereby a gene having an mRNA level 4 affected in response to the first reference compound but not the second reference compound is identified as having a response specific for the first reference compound.
- a further aspect of the invention is a method for grouping test compounds into classes, the method comprising: (a) exposing a cell culture or cell cultures comprising at least two gene-cell combinations to a test compound to generate exposed cell cultures, wherein at least one gene in the at least two gene-cell combinations is differentially expressed in a first and second reference state, to generate exposed cell cultures;
- RNA from the exposed cell culture or cultures (b) preparing RNA from the exposed cell culture or cultures; (c) screening RNA from (b) for mRNA levels of each gene in the gene-cell combinations of (a) to generate a gene expression fingerprint (GEF) for the test compound;
- GEF gene expression fingerprint
- At least one of the first and second reference states is a disease state such as cancer.
- the invention provides a method of generating a reference gene expression fingerprint (GEF) for at least one reference compound for use in grouping test compounds into classes, said method comprising:
- identifying at least two gene-cell combinations each of said at least two gene-cell combinations comprising a unique combination of a particular gene and a cell of a particular cell type, wherein a first gene-cell combination is identified by: (i) exposing host cells in vivo or a host cell culture of a first cell type to a first reference compound;
- RNA of (ii) comparing the RNA of (ii) to RNA prepared from host cells in vivo or a host cell culture of the first cell type not exposed to the first reference compound, wherein a change in a level of mRNA for a gene in cells of the first cell type in response to the first reference compound identifies the gene and cells of the first cell type as the first gene-cell combination for grouping test compounds into classes; and wherein a second gene-cell combination is identified by: 5
- RNA preparation (v) preparing RNA from the exposed host cells in vivo or the host cell culture of (iv); (vi) comparing the RNA of (v) to RNA prepared from host cells in vivo or a host cell culture of the same cell type as in (iv) not exposed to the first reference compound, wherein a gene having an mRNA level changed in response to the first reference compound is identified as a gene for use in the second gene-cell combination for grouping test compounds into classes, said second gene-cell combination being different from said first gene-cell combination and comprising the identified gene and cells of the same cell type as in (iv); and
- the invention provides a method for grouping test compounds into classes, said method comprising:
- test compounds are grouped into at least two classes based on differences or similarities between their GEFs and the reference GEF. 6
- Figure 1 comprises Figures 1A and IB.
- Figure 1A is a graphical depiction of GEF results for a reference compound (Ref) and test compounds x, y, z in two assays.
- Figure IB depicts GEF results for a Reference (Ref) compound and seven test compounds in three assays. Each of the squares represents the results of one assay. Activity of a compound in a particular assay is indicated by a solid square. Inactive compounds are indicated by an open square.
- Figure 2 comprises Figures 2A and 2B.
- Figure 2A depicts GEF results for a Reference (Ref) compound and six test compounds in five assays.
- Figure 2B is a single linkage tree diagram showing the percent disagreement between the reference and six test compounds with the GEF activity results depicted in Figure 2A.
- Figure 3 comprises Figures 3A-3C.
- Figure 3 A shows consensus GEFs for human breast cells from normal and different stages in malignant progression. Consensus gene expression changes representative of all of the cell lines classified as either weakly or highly invasive are graphically depicted. The values correspond to the median fold-change relative to the MCFIOA reference observed for each gene from data in Tables 7A-7B. The data shown for the "normal" GEF are changes in gene expression observed in the 76N MEC strain relative to MCFIOA.
- Genes with expression changes that are "tumor-associated" are represented by bars with left-handed stripes (bars having a stripe angling downward from left to right), genes associated with weakly invasive cancers have solid bars, and genes associated with highly invasive cancers with right- handed stripes (bars having a stripe angling upward from left to right) .
- the stippled bars denote genes whose direction or extent of expression change is associated with either weakly or highly invasive cancers.
- the figure legend to the right of the three graphs lists the genes depicted. Each number on the legend identifies a particular gene.
- Figure 3B shows GEFs of two breast cell lines with unknown invasive activity. Changes in gene expression of the breast fibroadenoma cell line 006FA2B and the breast epithelial cell line HBLIOO relative to MCFIOA were determined using Atlas I cDNA hybridization arrays. Data are shown for the 28 genes shown in the figure legend in Figure 3 A.
- the graphical representation of a particular bar (left-handed stripe, right- handed strip, stippled, or solid) has the same meaning as set forth above for Figure 3 A.
- Figure 3C depicts GEFs for tumor biopsy specimens. Gene expression was monitored by analysis of tumor RNA using Atlas I cDNA hybridization arrays. Changes in gene expression relative to a normal breast tissue specimen for the 28 genes 7 listed in the figure legend of Figure 3A are shown.
- the graphical representation of a particular bar (left-handed stripe, right-handed strip, stippled, or solid) has the same meaning as set forth above for Figure 3 A.
- Figure 4 shows gene expression changes following treatment of MDA231 with various compounds.
- MDA231 cells were exposed to taxol, butyrate, mevastatin, or vehicle control for 72 h and analysed for effects on gene expression as described in M&M. The data shown correspond to effects on mRNA levels elicited by drug treatment relative to control for those genes that had greater than 2-fold changes in expression in at least one treatment condition.
- the instant invention is directed to screening methods that allow the grouping of compounds into classes of compounds with similar activity (s), as measured by the changes elicited by the compounds in the expression of certain genes in certain cells.
- s similar activity
- the certain genes or cells employed in the analysis be identified by function, map location, or other parameter physiologically relevant to a disease or indication for which a therapeutic drug is intended or sought.
- GEF gene expression fingerprint
- a “gene-cell combination” as used herein refers to a particular gene in a particular host cell type. Different gene-cell combinations can arise from various combinations of particular genes and particular host cell types, such as the same gene in two or more host cell types, two or more different genes in the same host cell type, and so on. In addition, a single host cell may comprise one or more such genes to generate two or more gene-cell combinations.
- a host cell type as used herein refers to a cell of a particular source, such as but not limited to tissue of origin, state of differentiation, adaptation to particular 8 growth conditions, clonal variants, cell line, transformation, transduction, viral infection, parasite infection, bacterial infection, transgenic host, species of origin, and so on.
- a reference GEF is generated for a reference compound by exposing a cell culture or cultures comprising at least two gene- cell combinations to the reference compound and observing a change in the mRNA level(s) of the gene(s) in the gene-cell combinations in response to the reference compound.
- a single gene-cell combination is considered insufficient to generate a GEF.
- several gene-cell combinations are examined in response to the reference compound or in comparison of reference states to generate a "reference GEF" .
- the relative mRNA levels of at least one gene are compared in at least two host cell sources, wherein each host cell source comprises a different reference state to generate a reference GEF for a reference state.
- the genes are chosen on the basis of being differentially expressed in a first and second reference state.
- at least one of the reference states is a disease state.
- test compounds or agents such as libraries of peptides, peptidomimetics (such as, but not limited to p53, estrogen, raloxifene, tamoxifen, or IFN/3 mimetics), polypeptides, proteins, ribozymes, nucleic acids, oligonucleotides, or other organic or inorganic compounds, or natural products (e.g.
- microbial broths, plant or animal cell extracts are subjected to a screening process in which a GEF is generated for each test compound by exposing a cell culture or cultures comprising at least two gene-cell combinations to each compound and observing any changes in the mRNA level(s) of the gene(s) in the gene- cell combinations in response to the test compound.
- the results are used to compare similarities and differences among the test compounds screened. Based on these similarities or differences, the test compounds are divided into groups for further analysis. Such further analysis may involve in vivo testing or further screening in other assays.
- the methods of the invention are useful to identify compounds or agents that, for example, are mimetics of protein function (e.g.
- the "reference GEF” is preferably derived from the differential gene expression patterns observed between different cell states (e.g. , p53 positive vs. negative; metastatic vs. non-malignant tumors) and not necessarily from treatment with a reference compound per se.
- the reference compound may comprise a protein, polypeptide, peptide, nucleic acid, peptidomimetic, ribozyme, nucleic acid, oligonucleotide, or other organic or inorganic compound, or microbial, plant, and animal natural products.
- the reference compound is preferably chosen as having a representative in vivo activity, such as, but not limited to, inhibition of cell growth, stimulation of a receptor of interest, catalysis of a compound of interest, synthesis of a compound of interest, inhibition of replication of a virus of interest, stimulation of cell growth, inhibition of cell invasion of extracellular matrix, chemotactic response, anti- metastatic activity, anti-atherosclerotic activity, anti-inflammatory activity, anti-apoptotic effects, prevention of atherosclerotic lesion progression, decreased bone loss, decreased inflammation in rheumatoid arthritis, improved cognitive function, or prevention of hot flushes.
- the GEF generated for the reference compound need not directly be a measure of such activity.
- the GEF need only be representative of the effect on mRNA levels of the reference compound in a given gene-cell combination, or set of gene-cell combinations.
- the genes assayed for mRNA levels need not be directly or indirectly involved with the desired in vivo activity.
- test compounds are screened to allow grouping into classes relative to the reference compound. Members of such classes can then be screened for the desired in vivo activity, lack of side effects, or other improved features.
- a reference compound is chosen on the basis of the problem to be addressed.
- a reference drug, chemical compound, protein, peptide, oligonucleotide, etc. that has a known or predictable physiological effect relevant to a pathological state or desired pharmacologic property is selected as a basis for identification of a class of compounds.
- Some exemplary reference compounds include but are not limited to tamoxifen, raloxifene, interferon (IFN ⁇ ), interferon ⁇ (IFN ), interferon y (IFN ⁇ ), or an anti-Ha-ras-ribozyme (Kijima et al. , Pharmacol. Ther. 68:247-267 (1995)); ligands 10 for nuclear receptors that are transcription factors, such as steroid hormones, retinoids, etc.
- receptors such as endothelin; ligands for transmembrane receptors, such as endothelin, gastrin releasing peptide, neuregulin, PDGF, cytokines, chemokines, and insulin; extracellular matrix components such as vitronectin, laminin, and collagen; cell adhesion molecules such as N-CAM or I-CAM; inhibitors or activators of an enzyme of interest, such as L-NAME for nitric oxide synthase; chemotherapeutic agents, such as cisplatin or taxol.
- receptors such as endothelin
- ligands for transmembrane receptors such as endothelin, gastrin releasing peptide, neuregulin, PDGF, cytokines, chemokines, and insulin
- extracellular matrix components such as vitronectin, laminin, and collagen
- cell adhesion molecules such as N-CAM or I-CAM
- inhibitors or activators of an enzyme of interest such as
- a reference compound can also be the product of a gene expressed within a host cell.
- genes may be endogenous or heterologous, under the control of an endogenous or heterologous promoter, etc.
- Exemplary genes include, but are not limited to transgenes, viral genes, antisense nucleic acids, ribozymes, etc.
- a reference state will be employed instead of, or in conjunction with, a reference compound for the determination of the reference GEF.
- the differences in mRNA levels between two or more cells or tissues representing relevant physiological/pathological states form the basis of a reference GEF.
- Some examples of reference states include, but are not limited to, normal vs. atherosclerotic blood vessels of varying lesion severity; normal vs. progressive stages in the development of malignant carcinomas, sarcomas, melanomas, or lymphomas; normal vs. stages of neurodegeneration associated with different types and severity of Multiple Sclerosis, Alzheimer's or Parkinson's disease.
- the instant invention utilizes changes in the mRNA levels of one or more genes in at least two gene-cell combinations, wherein the mRNA level of the gene(s) is responsive to the reference compound, to generate a GEF for each test compound screened.
- the test compounds may affect mRNA levels directly or indirectly, by, for example, binding to a promoter or other regulatory element, binding to a receptor and triggering some intracellular signal, altering the stability of the mRNA, binding to an intracellular enzyme, such as a kinase or phosphatase, binding to a transcription factor, altering the redox environment, or affecting ion flux into and within the cell.
- the genes are preferably endogenous genes under the control of their native promoters.
- cells may be infected with viruses, wherein the responsive genes are viral genes.
- a marker gene such as a heterologous gene under control 11 of a heterologous promoter, is introduced into the cell as an internal control for monitoring gene expression or the physiological state of the cell.
- the set of one or more responsive genes for screening may be determined in many ways.
- the mRNA from a cell culture exposed to a reference compound can be compared to mRNA from a control, or unexposed cell culture.
- an organism or animal is exposed to a reference compound in vivo, and the organism, tissue samples, explants, primary cultures, or the like used as the source for mRNA.
- Changes in the level of specific mRNA that occur in response to the reference compound can be identified by a variety of means, including but not limited to subtractive hybridization using either normalized or unnormalized libraries (e.g. ,
- genes known to be responsive to the reference compound may comprise all or part of the set of responsive genes.
- genes known to be responsive to the reference compound may comprise all or part of the set of responsive genes.
- Such genes may be identified from the literature, from cloning of cDNAs from cell cultures exposed to the reference compound, or other source.
- epidermal growth factor-regulated genes such as junB, rhoB, EGF receptor, integrin beta 1 , and viculin may comprise all or a part of a set of genes to screen candidate compounds for selective EGF receptor agonists or antagonists.
- genes encoding such proteins as p21, MDR1, hsp70, IGFBP-3, and bax have all been shown to be regulated by p53 through different mechanisms. These genes may comprise all or a part of a set of genes to screen candidate compounds for p53 mimetics.
- a responsive gene chosen for use in the screening assay sustains at least a two to fivefold change in the level of its mRNA in response to the reference compound. This change may be an increase or decrease.
- the measure of fivefold or greater responsiveness provides for the detection of "weakly " active test compounds which may, for example, provide only a "partial” response (e.g. , a two-fold change in mRNA levels in comparison with a "full” response that is five-fold). 12
- the same set of responsive genes, or a subset thereof, or yet a different set is examined in more than one cell type as part of the screening (i.e. , to generate different "gene-cell combinations").
- gene-cell combinations Preferably two to 15 or more gene-cell combinations (or "assays") are used in screening compounds.
- the number of assays used to characterize compounds or reference states into groups based on GEF can be reduced using additional reference compounds with known in vivo effects. GEF's can be interpreted as like or unlike the reference compound or state. For example, when the additional reference compound has undesirable in vivo effects, assays which fail to distinguish the additional reference compound from the first reference compound may be eliminated from the screening used to generate GEFs.
- Some of the gene-cell combinations may be internal controls. For example, "house-keeping" genes such as GAPDH, actin, or cyclophilin are typically expected not to respond to the reference compound and thus can serve as negative internal controls. Positive internal controls can comprise, for example, a recombinant molecule under control of a promoter expected or known to be responsive to the reference compound.
- Additional internal controls can comprise genes which are predictive of possible "toxic" effects of the reference or test compounds.
- control responsive genes include but are not limited to cytokines such as TNF or lymphotoxin, heat shock proteins such as hsp70, DNA damage inducible genes such as gaddl53 or gadd45, and the like.
- An increase in the mRNA level of one or more of these genes is typically predictive of a toxic effect of the reference or test compound.
- screening of test compounds for reduced toxic effects is accomplished by looking for reduced or unchanged levels of these internal control genes.
- tissue explants or clinical samples such as primary cell cultures, tissue explants from experimental animals, or clinical specimens such as blood samples, tumor biopsies, atherosclerotic blood vessels from a patient are preferred.
- tissue explants or clinical samples such as primary cell cultures, tissue explants from experimental animals, or clinical specimens such as blood samples, tumor biopsies, atherosclerotic blood vessels from a patient are preferred.
- test compounds preferably in the form of a library
- a library of about 10 5 -10 7 test compounds e.g. , peptides, oligonucleotides, ribozymes, peptidomimetics, polypeptides, proteins, nucleic acids, oligonucleotides, or other organic or inorganic compounds, etc.
- test compounds e.g. , peptides, oligonucleotides, ribozymes, peptidomimetics, polypeptides, proteins, nucleic acids, oligonucleotides, or other organic or inorganic compounds, etc.
- a small molecule library is screened by exposing cell cultures to a typical final concentration of test compound of 1 - 10 ⁇ M.
- a range of concentrations e.g.
- the cell culture treatment may be in 96 well microtiter dishes. Exposure is typically done for a period of 24 to 48 hours, but can be as short as 30 minutes or as long as a week, especially in the case of transfected or infected cells.
- the cells are usually treated in a humidified environment containing 5 to 10% CO 2 at 37°C, but variations on these conditions may be warranted by the specific screen.
- RNA is then recovered from the exposed cultures by methods well known in the art, preferably by a method readily adapted to high throughput (e.g.
- RNA may be optionally reverse-transcribed into cDNA.
- the mRNA or cDNA can be used as probe or as target in hybridization reactions, and may be immobilized or in solution.
- Messenger RNA from the set of one to twenty or more responsive genes can be quantitated by methods well known in the art using such exemplary techniques as standard Northern or slot blot hybridization, nuclease protection, or quantitative PCR which are limited in the number of different RNAs that can be simultaneously analyzed as well as in their amenability to automation.
- Other preferred methodologies employ isotopically or fluorescently-labeled RNA or cDNA prepared from the isolated cellular RNA as hybridization probes for arrays containing purified cDNAs spotted onto membrane filters (e.g. , Bernard et al. , Nucl. Acids Res. 14
- the GEF for each compound comprises the results of the screening procedures. Compounds may be eliminated from further testing because of the likelihood of toxic effects on the cell, nonspecific responses elicited, and so on.
- the GEF may be further modified by further testing with additional responsive gene - cell combinations , by using the same set of responsive genes and cells but different concentrations of test compounds, eliminating uninformative responsive gene-cell combinations from the GEF, and so on.
- Test compounds screened as discussed above are then sorted into classes based on their GEFs. For example, test compounds which elicited a change in mRNA levels of all members of a set of responsive gene-cell combination would be grouped separately from test compounds which elicited a change in only one instance, two instances, etc. As the number of assays used for screening increases, more grouping becomes possible.
- the reference compound is defined as being "active" in all GEF assays; activity can be an increase or decrease, relative to control, in the mRNA level for the particular gene following compound treatment.
- a compound x or y is discovered or identified by having activity in at least one GEF assay. Compounds x and y are categorized separately from the reference compound based upon inactivity in at least one assay.
- Compounds are categorized with each other if they are active in the same assays.
- four possible categories of compound can be defined.
- the number of possible categories is equal to x n , where x is the number of activity states measured (e.g. + and -) and n is the number 15 of assays.
- x n 2 2 or 4 possibilities, represented by the reference and compounds x, y, z.
- Each compound is distinguishable from the others by a different GEF.
- the categories can be further refined by considering quantitative differences in the response to different compounds as a criterion for classification. By increasing the number of GEF assays that are evaluated, more categories of compounds can be defined.
- the compounds with activity in only one assay are not categorized or further evaluated unless they are active in assays that form the basis for the majority of the active compounds identified (indicating that they may be affecting a portion of the same signaling pathway).
- compounds y and b would be potential candidates for further evaluation because they are active in assays that identify compounds x, a, and z.
- Compound c would not be further tested.
- the decision to increase the stringency for categorization can be influenced by the pattern of gene expression observed as well as data from other assays. For 16 example, in Figure 2 A if evaluation of compounds x, z, and a revealed that only x and z were active in an important cell-based assay, compounds such as b and y which demonstrate activity in assays common to x and z would be further evaluated alone and in combination.
- representative compounds can be further characterized in cell-based assays well known in the art for properties of interest.
- assays might include, for example, inhibiting or stimulating effects on cell growth, anti- viral activity, gel electrophoretic mobility shift assays with D ⁇ A-protein complexes prepared from extracts of treated cells, cell invasion through extracellular matrix or reconstituted basement membrane, anchorage-independent growth, chemotaxis, apoptosis, differentiation, cell adhesion to various substrata, cell-cell interactions, secretion, proteolytic activity, osteoclastic bone resorption, etc. It is advantageous in some instances to extend the cell -based assay to animal models where available.
- animal models known in the art include animal models for uterotropic effects (e.g. , uterine hypertrophy; Allen-Doisey), fever (e.g. , rabbit pyrogenicity), osteoporosis (e.g. , rat cortical and trabecular bone density following ovariectomy or transgenic/knock-out animals), atherosclerosis (e.g. , lipid deposition in blood vessels of rabbits fed lipid-rich diets or in transgenic/knock-out animals), restenosis (e.g. , neo-intimal thickening following carotid injury), cancer (e.g.
- tumor induction in rats or mice tumor xenograft growth in nude, athymic or in transgenic/knock-out mice
- metastasis e.g. , lung colonization following tail vein injection of tumor cells
- rheumatoid arthritis e.g. , adjuvant-induced joint swelling
- multiple sclerosis e.g. , EAE model in marmosets or rats, transgenic/knock-out mice
- Alzheimers disease e.g. , transgenic/knock-out mice
- the GEF's of two or more test compounds may complement each other, i.e. , when the GEF's are superimposed they approximate that of the reference compound or desired aspects of the GEF of the reference compound.
- the two or more test compounds may be used together in combination in cell-based or in vivo assays to determine whether the combination has desired bioactivity.
- estrogen receptor which is a ligand- inducible transcription factor (Mangelsdorf et al. , Cell 83:835-839 (1995)
- ER estrogen receptor
- Mangelsdorf et al. Cell 83:835-839 (1995)
- regulation of gene expression by estrogen occurs by a limited number of mechanistically different processes that may be further modified in a tissue-specific manner, and compounds that have selective in vivo effects will elicit distinguishable gene expression patterns.
- ER ligand binding and cell-based estrogen (E)-dependent proliferation assays include standard ER ligand binding and cell-based estrogen (E)-dependent proliferation assays, or ER-mediated transactivation assays (e.g. , Tzukerman et al , Mol. Endo. 8:21-30 (1994)), which utilize different E-responsive promoters to characterize compounds.
- Screening for ligands that differ in their abilities to change ER conformation is possible using a proteolytic fragmentation assay (Beekman et al. , Mol. Endo. 7: 1266-1274 (1993)). Prudent use of these assays can permit the separation of E agonists from partial agonists and antagonists.
- these methods do not provide sufficient information about a compound to enable prediction of in vivo selectivity since compounds with markedly different in vivo effects are not distinguishable by those assays.
- a method to classify compounds based upon differential gene expression modulation was developed herein to identify such selective compounds.
- a total of forty-nine compounds was tested by this method and thereby categorized into classes 18 based upon their GEFs.
- the in vivo activities of some of the sorted compounds were evaluated to determine the predictability of the in vitro "fingerprint" for in vivo effects.
- E-responsive genes were identified by literature search (52kD cathepsin D, growth hormone, prolactin, progesterone receptor, pS2, TGFalpha, IGFBP-1, CBG, Amphiregulin, TRHR (thyroid releasing hormone receptor)) and the corresponding cDNA (or fragments thereof) were cloned and probe fragments prepared for Northern or slot blot hybridization studies by techniques known in the art.
- Mammalian cell lines that contain endogenous ER were identified through literature reports (GH3 pituitary adenoma, BG-1 ovarian carcinoma, MCF7 breast carcinoma, ZR75-1 breast carcinoma, MDA361 breast carcinoma, Ishikawa human endometrial carcinoma (Nishida et al.
- ER expression e.g. , protein by Western blot analysis; RNA by RT-PCR.
- transfected cells which stably express ER were also tested (MDA231-ER-breast carcinoma (Zajchowski et al , Cancer Res. 53:5004-5011 (1993)), 185B5-ER— human mammary epithelial cell line (Zajchowski et al , Mol. Endocrin.
- the first step was to determine which of the genes and cell lines actually showed measurable responses to E treatment.
- ER-positive cells were grown in estrogen-free culture medium and treated with the natural hormone, 173-estradiol (E2), or 17 ⁇ -ethinyl-estradiol (EE; non-metabolizable estrogen) for short (3h), intermediate (24h) , and long (72h) time periods and RNA prepared from the cells at each time point. Analysis of the levels of mRNA for the genes of interest gave an estimate of the kinetics of the response to EE treatment and an indication of the optimal conditions to measure the responsiveness of each gene.
- E2 173-estradiol
- EE 17 ⁇ -ethinyl-estradiol
- the same compounds can have different activities on different genes within the same cell (e.g. , PR compared to pS2 or TGF- ⁇ in the MDA-ER cells).
- the statistical probability of identifying raloxifene as an active compound in such a screen would be 96% if 20 assays are employed, 91 % if 15 assays are used, and 80% if only 10 are analyzed (Snedecor et al , Statistical Methods, 8th ed. Iowa State University Press, Ames, Iowa, Chapter 7, (1989)). To simplify the GEF screen, additional studies were performed to determine which of the redundant assays was most amenable to screening strategies (e.g. , highest reproducibility and extent of change relative to control).
- the IGFBP-1/Fe33 gene-cell combination (representing pattern V) was not employed in further studies (due to difficulties interpreting data in these liver carcinoma-derived cells, where drug- metabolizing activity is significant).
- the chosen representative assays for subsequent studies are shown in Table 2. This representation of the data shows that each compound is identified by a specific GEF based upon the activity elicited in each of the four assays (seen as + and - pattern of activity in the column underneath each compound). In this manner, compounds with identical GEFs were grouped together and were distinguishable from those with different GEFs. For example, E2, EE, and 2HE were placed in one group (#1 in Table 2) and HT and RU in another (#2). Of utmost importance was the observed difference between E2, Ral, and HT, which indicated that these assays are successful in discriminating among compounds with distinct in vivo pharmacologies. 22
- This method of classification was employed to separate an additional thirty compounds, many of which are structurally related to the first nine compounds tested.
- Compounds El (estrone), E3 (estriol), DHE (17 ⁇ -dihydroequilen), DHEN (17 ⁇ - dihydroequilenin), ZK182491 and ZK155843 are derivatives of either 17 ⁇ -estradiol (17c-- E2) or 17/3-estradiol.
- Compounds ZK166780, ZK166781, ZK167466, ZK167957, and ZK180686 are 11/3-substituted 173-estradiol derivatives related to RU39411.
- Compounds HT, ZK186275, ZK183819, ZK182956, and ZK183955 are tamoxifen derivatives.
- Compounds ZK185157 and ICI182780 are related to the pure steroidal antagonist, ICI164384.
- Compounds ZK182254, ZK186217, and raloxifene are benzothiophenes.
- Compounds ZK183659, ZK22496, and ZK185704 are structurally related (i.e. , contain a cyclophenyl moiety).
- Compound ZK167502 is a napthalene derivative and coumestrol is a phytoestrogen (Price et al. , Food Addit. Contain. 2:73-106 (1985)). Many of these had been previously classified as agonists, partial agonists, or antagonists of the ER through assays of ER binding and transcriptional activation. In these experiments, compounds were scored using three activity levels (i.e. , inactive, partially active as ⁇ 50% of the E2 response, fully active as > 50% of the E2 response). As is evident from Table 3, the compounds could be divided into ten groups by this analysis (see Table 3) . This separation of compounds is not based primarily upon chemical structure as indicated by the results with the compounds that are related to RU39411 (i.e. ,
- E2 tamoxifen, raloxifene, ICI 164384
- E2 tamoxifen, raloxifene, ICI 164384
- E2 tamoxifen, and raloxifene, but not ICI, have "estrogenic" effects on the bone and cardiovascular system in experimental and/ or clinical studies (i.e. , they are effective in attenuating atherosclerotic lesion formation tamoxifen: Williams et al. , Arterioscler.
- MDA-231 ER transfectant E-28 cells were routinely cultured in phenol red-free alpha-modified minimal essential medium (MEM Gibco BRL; Gaithersburg, MD) supplemented with 1 milliMolar (mM) HEPES, 2mM glutamine, 0.1 mM MEM non-essential amino acids, 1.0 mM sodium pyruvate, 50 ⁇ g/ml gentamicin (all from Gibco), 1.0 microgram/milliliter ( ⁇ g/ml) insulin (Sigma; St. Louis, MO), and 5% DCC-treated FBS (Intergen). Cells were plated at approximately 40% confluency (1.5 x 10°/plate) in 150 mm culture dishes. Following an overnight cell attachment, the medium was changed to include 0.2% ethanol or the test compounds and cultured for an additional 48 hours (h).
- MEM Gibco BRL Gaithersburg, MD
- GH3 rat pituitary cells were routinely cultured in DMEM-F10 (1: 1) medium containing 12.5% horse serum, 2.5% FBS, 25 mM Hepes, 2 mM L-glutamine, and 50 ⁇ g/ml gentamicin sulfate at 37°C, 5% CO 2 . Under these conditions, the cells were partially adherent, and both adherent and non- adherent cells were maintained during the passaging of the cells.
- mRNA expression cells were seeded (10 6 /100 mm dish) in culture medium without phenol red and containing DCC-treated serum. After 3 days, the medium was changed to one containing 0.2% ethanol or the test compounds, and the cells were further incubated for 2 days.
- BG-1 human ovarian carcinoma cells (Geisinger et al , Cancer 63:280-288
- DMEM:F12(1: 1) medium containing 10% FBS, 2 mM L-glutamine and 50 ⁇ g/ml gentamicin sulfate.
- FBS fetal bovine serum
- 2 mM L-glutamine fetal calf serum
- 50 ⁇ g/ml gentamicin sulfate 50 ⁇ g/ml gentamicin sulfate.
- cells were cultured for 24h in phenol red-free medium containing 5% DCC-treated FBS prior to plating in the same medium at a density of 2 x 10 6 /150 mm plate. The following day, the medium was changed to include 0.2% ethanol or the test compounds and cultured for an additional 72h.
- ZR75-1, MCF7, and MDA361 human breast carcinoma cell lines were routinely cultured in alpha-modified MEM supplemented with 1 mM HEPES, 2 mM glutamine, 0.1 mM MEM non-essential amino acids, 1.0 mM sodium pyruvate, 50 ⁇ g/ml gentamicin, 1.0 ⁇ g/ml insulin, and 10% FBS. Cells were plated (ZR75-1: 1.5 x
- the HepG2 human hepatocarcinoma cells stably transfected with ER (clones ER1 and ER2), were cultured in EMEM (GIBCO), supplemented with 1 mM HEPES, 2 mM glutamine, 0.1 mM MEM non-essential amino acids, 1.0 mM sodium pyruvate, 50 ⁇ g/ml gentamicin, and 10% FBS.
- EMEM EM
- Ishikawa human endometrial carcinoma cells were cultured in EMEM with 2 mM glutamine, 50 ⁇ g/ml gentamicin, and 10% FBS.
- Fe33 ER-transfected FTO-2B rat hepatoma cells
- DMEM- Ham's F12 (1: 1) without phenol red containing 10% DCC-FBS on 0.1 % gelatin coated Petri dishes. All cells were plated (HepG2-ER: 4 x lOVplOO; Ishikawa: 2 x 10 6 /pl50; Fe33: 2.5 x 10 5 /pl50) in phenol red and insulin-free media containing 5% FBS-DCC for the assays. Following an overnight cell attachment, the medium was changed to include 0.2% ethanol or the test compounds and cultured for an additional 72h.
- B5-ER ER-transfected human mammary epithelial cells
- RNA Isolation and Slot Blot Analyses At the end of the compound treatment time, cell mono layers were harvested into Ultraspec (Biotecx Laboratories, Houston, TX) or RNeasy (Qiagen Inc. , Santa Clara, CA) RNA isolation reagent and processed according to the manufacturer's suggested protocol. Total RNA (MDA-231 ER: 10 ⁇ g; GH3: 1.0 ⁇ g) was spotted onto a Zetaprobe-GT nylon membrane using a 48-well slot blot apparatus attached to a vacuum manifold. Total RNA (20 ⁇ g) from treated and untreated samples of all of the other cell lines was evaluated by Northern blot analysis.
- Hybridization of the membranes to 32 P-dCTP labeled probes was carried out as previously described. Quantitation of the specific hybridization in each spot by subtracting non-specific background detected in a negative control for each mRNA was performed using a Fuji phosphorimager; the ratio of the signal intensities in compound-treated samples relative to controls provided the value for fold-change used in the assessment of the compound activity for each particular assay. Changes in mRNA levels greater than or equal to 2-fold were scored as positive. 28
- RNA samples were diluted to 20 ng/ ⁇ l in DEPC-treated water. RT PCR was performed using 100 ng total RNA.
- the reaction mixtures contained 5 units ⁇ Tth DNA Polymerase (Perkin Elmer; Foster City, CA), IX EZ buffer (Perkin Elmer; Foster City, CA), 2.5 mM Mn(OAc) 2 , 300 ⁇ M dNTP's (mix from Pharmacia; Alameda, CA) and 10 pmol of each biotinylated primer in a final volume of 50 ⁇ l.
- PCR primers PR#1 (5' GTC AGT GGR CAG ATG CTR TAT TT), PR#2 (5'-l lC TTC AGA CAT CAT TTC YGG AAA TTC) were synthesized by Synthetic Genetics (San Diego, CA). Amplification consisted of a 30 minute RT step at 60°C immediately followed by 33 cycles of a two step PCR reaction (95 °C for 15 seconds, 60 °C for 45 seconds) and a final 7 minute extension at 60 C in a Perkin Elmer 9600. Following PCR, 1/20 reaction volume is removed and quantitated using streptavidin-coated 96-well microplates and oligonucleotide probes specific for the PCR target.
- the probe is coupled to either HRP or AP and addition of either colorimetric (HRP) or chemiluminescent (AP) substrates permits quantitation of 300-500 initial copies of specific RNA template in a 20-100 ng total RNA sample.
- HRP colorimetric
- AP chemiluminescent
- vt ' tro-transcribed PR mRNA was used to generate standard curves (calculated by non-linear regression analysis using a four parameter sigmoidal plot) for quantitation of the amount of PR mRNA in each reaction. Changes in mRNA levels were scored as positive if they were greater than or equal to 3-fold.
- Sprague-Dawley rats weighing 35-50 g. were given daily subcutaneous injections for three days with compounds or vehicle alone.
- the compounds were dissolved in a vehicle consisting of 10% ethanol in arachis oil or a mixture of benzylbenzoate/ castor oil (1:4).
- the uteri were excised and placed in neutral buffered 3.7% formaldehyde for a minimum of 24 hours. The uteri were then embedded in paraffin, cut into 4- ⁇ m transverse sections, and stained with hematoxylin and eosin and the sections evaluated for luminal epithelium cell height as described by Branham et al. (Branham et al. , Biol. Reprod.
- IFN/3 has efficacy in the treatment of Multiple Sclerosis (MS) (The IFN/3 Multiple Sclerosis Study Group Neurology 43:655-661 (1993)). The precise mechanism by which IFN/3 elicits its therapeutic efficacy is unknown. However, a great deal of knowledge exists concerning the signal transduction pathways modulated by IFN/3; as a ligand, IFN/3 directly interacts with its receptor to induce phosphorylation of a number of signal transducing proteins (STATs (Ihle, Nature 377:591-594 (1995)) and eventually direct specific changes in gene expression (Darnell et al , Science 264: 1415-1421 (1994)).
- STATs Ihle, Nature 377:591-594 (1995)
- IFN ⁇ A homologous member of the same family of cytokines, IFN ⁇ , is capable of binding the same receptor protein yet cannot be used in the treatment of MS due to its unacceptable side effect profile.
- Another interferon, IFN7 shares some of IFN/3 's effects on gene expression, yet actually exacerbates the symptoms of MS (Panitch et al. , J. Neuroimmunol. 46: 155-164 (1993)). Therefore, differences in the biological effects of 30 these three ligands can be exploited in developing screens to identify selective IFN/3 mimetics that might be more efficacious and have better tolerability than IFN/3 itself. Animal models to test drug efficacy in ameliorating the severity of this disease exist ( . e. , Experimental Autoimmune Encephalitis (EAE) or T cell transfer EAE model) .
- EAE Experimental Autoimmune Encephalitis
- T cell transfer EAE model T cell transfer EAE model
- RNA is prepared from candidate cell lines that have been treated with IFN/3 and used to estimate the number of differentially expressed sequences by hybridizing probes prepared from this RNA on microarrays containing 100 or more pre-selected cDNAs, such as the Atlas cDNA Arrays (i.e. , Clontech).
- the cell lines that show the largest number of differentially expressed sequences are chosen for studies to identify IFN/3-responsive genes. Technically, this can be approached through any available differential gene expression screening strategy (e.g. , DD-PCR, subtractive hybridization libraries, etc.). Subsequent to identification of the differentially-expressed genes, limited optimization is preferred to determine whether conditions such as time of treatment can enhance the extent of mRNA change relative to control. Conditions amenable to analysis of the largest number of genes are used.
- genes that show significant regulation are used in screens with a set of compounds known to have different, but overlapping effects in common with IFN/3 (e.g. , IFN , IFN ⁇ , IL-8, IL-12).
- This evaluation can be carried out by arraying the cDNAs for these candidate genes and using RNA isolated from each of the compound-treated cells to prepare hybridization probes. Responsive genes are evaluated for the response to each compound.
- An exemplary set of one or more genes, including gene/cell combinations responds only to IFN/3, another group of genes responds to both IFNo. and ⁇ , another with IL-8, IFN ⁇ , and IFN/3, etc. 31
- the “best” gene/cell combination (greatest fold response and signal-to-noise ratio for detection; gene expression measurable in cell line where other "informative" genes are measured) from each group of genes is chosen for the compound screen.
- Internal control genes are designated in the cell line to be used as indicators of cytotoxicity (e.g. , gadd45, hsp 70).
- test compound library is screened for those test compounds which are specific modulators of IFN-responsive genes using a scoring method of active and inactive.
- the "active" hits are those that elicit changes in gene expression significantly above the background variance of the specific assay.
- Test compounds are then grouped according to their GEF and re-tested to determine the EC 50 for representative compounds. At this stage in the generation of a GEF that will be predictive for in vivo efficacy, it may not be clear how close to the GEF of IFN/3 a "hit" will need to be in order to have IFN-like activity in vivo. To estimate this, test compounds that showed activity in the greatest number of assays ( . e.
- IFN responses e.g. , anti- viral effects
- This screen is employed as a way of sorting through GEFs to determine whether "hits" with activity in very few IFN-response assays have IFN-like activity. If none of the hits that are active in multiple GEF assays show activity in the bioassay, compounds are preferably screened in combination with each other to determine their GEF upon co- treatment. Combinations of compounds that generate new GEFs closer to that of IFN/3 are subsequently tested for in vitro activity in the bioassay.
- Representative compounds are selected for in vivo evaluation based upon their activity in in vitro bioassay s, potency in the GEF assays, and other available information. If any "hits” meet criteria for in vivo testing, they are evaluated for efficacy in the EAE model. If not, additional compound sources can be screened, or weak "hits" can be optimized against their GEF to find more potent compounds before testing in animal models. 32
- the GEF profile determined in the previous step can be used directly as a means of optimizing "lead” or representative best candidate compounds.
- EC50s and maximal responses for the derivative compounds for each assay are considered.
- the "lead” compound(s) is usually tested for adverse, undesirable effects in appropriate biological models (e.g. , induction of fever, testable in a rabbit pyrogenicity assay). If there are “lead” compounds that have different GEFs, the GEF corresponding to the "lead” which has little or no activity in this assay is used for further optimization. If, however, none of the “lead” compounds meet the selectivity requirements for the desired drug, it may be necessary to incorporate additional assays into the screening panel and re-test all of the bioactive "hits" ; in this new screen, compounds within the previously designated GEF classes may be differentiated from each other by these new assays (i.e. , due to a different GEF that is now discovered). In that case, additional in vivo evaluation is necessary to validate the predictability of the new GEF for in vivo efficacy and selectivity.
- additional in vivo evaluation is necessary to validate the predictability of the new GEF for in vivo efficacy and selectivity
- p53 In addition to its transcriptional regulatory activities, p53 has been shown to influence DNA replication and repair as well as apoptotic signaling pathways. A profile of the changes in gene expression that result from the expression of wild type (WT) p53 in a cancer cell will be used in the application presented here as a tool to search for compounds that mimic the activities of p53.
- WT wild type
- the existence of expression systems that enable investigator-control of protein expression (e.g. , lac or tet-inducible systems) as well as temperature sensitive (ts) p53 proteins and a number of p53 mutants enhance the suitability of this system for drug-screening efforts. 33
- RNA for this analysis is isolated from cells cultured under conditions where (1) the expression of the p53 protein is on or off (e.g. , in an inducible expression system) or (2) the active vs. inactive form of the p53 protein is present (e.g. , for a temperature sensitive p53 protein or for WT vs. mutant proteins).
- the effector compound is a 53kD protein (i.e. , p53) and not a small molecule ( . e. , estradiol) or a polypeptide ligand (/ ' . e. , IFN-/3) and (2) the search is for an alternative effector molecule(s) which elicits the same in vivo effects as p53, not a more selective or efficacious molecule.
- a successful p53 mimetic could be a combination of compounds, each of which perform a "subset" of the essential p53 functions.
- the cell line(s) which showed the greatest number of changes in response to the reference compound was chosen for the identification of responsive genes.
- a minimal set of gene/cell readouts that are predictive of p53's tumor suppressive function is the desired outcome of the assay selection step. Therefore, the initial gene identification approach will evaluate several different tumor cell lines whose tumorigenicity is suppressed by p53 introduction/activation. The p53-responsive assays that are shared by all of these cells are selected for further evaluation.
- An additional, but not essential, method for choosing the appropriate assays is to evaluate the expression of candidate genes following induction of the WT p53 compared to its mutated versions.
- Genes which are regulated by truncated or mutated p53 proteins that retain their tumor suppressor function are useful in a p53 mimetic screen since they are markers of desirable p53 functions; genes which continue to be regulated by mutant versions of p53 that are inactive in tumor suppression would be eliminated from the screen or used as "non-selective" assays.
- the "hits” can initially be tested in in vitro assays for proliferation (e.g. , measured by 3 H-thymidine uptake), anchorage-independent growth (e.g. , soft agar assays), and apoptosis (e.g. , measured by DNA-laddering induced upon exposure to radiation in the presence of the compound). This preliminary evaluation will further define the GEF that predicts activity in tumor suppression (as measured by the in vitro surrogate assays).
- the in vitro systems can be also used to evaluate efficacy of combinations of "hits" that may synergize to generate a GEF that predicts tumor suppressor function.
- Representative compounds are selected for in vivo evaluation based upon their activity in in vitro bioassay s, potency in the GEF assays, and other available information.
- the efficacy of compounds in suppressing the growth of human tumor xenografts in nude, athymic mice will be assessed as a measure of tumor-suppressive activity.
- Positive controls for this study are the same tumor cells which are engineered to express an inducible p53 protein, which enables regulation of tumor growth in vivo.
- the GEF profile that correlates with in vitro and in vivo efficacy can be used directly as a means of optimizing "lead” compounds. This is a preferred step for any combinations of compounds that are active in the in vitro bioassay s, since the combination therapy may be difficult to evaluate in in vivo assays due to possible pharmacokinetic differences of the components of the mixture. At this stage of analysis, EC50s and maximal responses for the derivative compounds for each assay are considered.
- a critical aspect in this progression is the process by which cells pass through the endothelial lining of the blood vessel and invade into the surrounding stroma.
- Cell invasion through a reconstituted basement membrane e.g. Matrigel
- the assay is not readily adaptable to the screening of large compound libraries.
- the GEF methodology can be used to develop a screen for agents that block or decrease cell invasion and/or metastasis.
- the genes for this screen are identified by comparing reference states.
- Exemplary reference states may include, but are not limited to the following: invasive vs. non- invasive cell lines, normal vs. invasive carcinoma tissue, or two histopathologically-staged malignant tissues (e.g., prostatic carcinomas of Gleason Grades III and IV).
- RNA messenger RNA
- An exemplary set of cell lines or strains for studies of breast cancer progression is based, for example, on reported in vitro invasive properties (e.g. , normal human mammary epithelial cells, immortal MCFIOA or 184B5, poorly invasive MCF7, ZR75-1, MDA468, moderately invasive MDA435, and highly invasive MDA231 or BT549 (available from ATCC, Rockville, MD).
- Tissue samples can include human xenografts from immunodeficient animals, biopsies that have been dissected by a pathologist to 36 specifically include tumor, normal, and invasive material or similarly characterized cells generated, for example, by Laser Capture Microdissection (Emmert-Buck et al. , Science 274: 998-1001 (1996)).
- Laser Capture Microdissection Emmert-Buck et al. , Science 274: 998-1001 (1996).
- RNA isolated from the normal and the most invasive cells can be compared using methods described above for identifying differences between treated and untreated cells (e.g.
- DD-PCR subtractive cDNA libraries
- high density cDNA arrays Pooled samples from normal vs. tumor cell lines or specimens representing different stages of cancer progression may also be used to generate this gene expression comparison and are, in fact, preferred because of the greater pool of differentially expressed sequences that is likely to be generated. This is particularly important with regard to the tumor cells, since it is known that there is individual variability in tumors; these differences are likely to be reflected in different gene expression profiles.
- genes that are differentially expressed between normal and highly invasive cells are selected for further evaluation.
- Genes identified as differentially expressed in the first step are assessed for inclusion in the GEF based upon their expression in the cells being considered for use in the screening process. For example, if the initial gene identification was carried out using RNA isolated from tissue specimens and not cell culture material, some genes expressed in vivo may not be similarly expressed or regulated in the culture environment. Preferably cell lines which express the greatest number and the highest levels of mRNA for the differentially expressed genes would be chosen for the GEF assays.
- regulation of expression of any of the candidate genes by agents that are reported to modulate cancer cell invasion is determined.
- the genes whose expression is affected by these agents are then included in the GEF.
- the "best" assays e.g. gene/ cell combination with greatest fold response and signal-to-noise ratio for detection
- Appropriate genes to be used as indicators of cytotoxicity e.g. gadd45, hsp 70
- internal controls e.g. , GAPDH
- the "hits” are initially tested in in vitro assays for invasion (e.g. modified Boyden chamber (Albini et al , Cancer Res. 47:3239-3245 (1987)). This preliminary evaluation further defines the GEF that predicts activity in tumor cell invasion (as measured by the in vitro surrogate assays) .
- the in vitro systems can also be used to evaluate efficacy of combinations of "hits" with different GEF that may demonstrate activity when mixed together but not when tested alone.
- Representative compounds are preferably selected for in vivo evaluation based upon their potency in the GEF assays.
- the efficacy of compounds in suppressing tumor invasion can be assessed by a number of methods, including metastatic growth of human tumor xenografts in nude, athymic mice or the invasion of tumor cells implanted on the renal capsule.
- the GEF profile that correlates with in vitro and in vivo efficacy can be used directly as a means of optimizing "lead” compounds. This will be an essential step for any combinations of compounds that are active in the in vitro bioassay s, since the combination therapy will be difficult to evaluate in in vivo assays due to probable 38 pharmacokinetic differences of the components of the mixture. At this stage of analysis, EC50s and maximal responses for the derivative compounds for each assay are considered.
- the progression of breast cancer (BC) from a hormone-dependent, well- differentiated carcinoma to a more advanced stage lesion is marked by the loss of estrogen receptor (ER) function, decreased estrogen-cadherin (E-cadherin) expression or function, and increased vimentin expression.
- This progression resembles the epifhelial- mesenchymal transition (EMT) (Hay, Acta Anat. 154:8-20 (1995)) that occurs during embryonic development.
- EMT epifhelial- mesenchymal transition
- the advanced stage breast cancer cells adopt structural and functional characteristics of mesenchymal cells. Altered expression of intermediate filament proteins contribute to this phenotype (e.g. , decreased expression relative to less advanced cancer cells of some keratins and the induction of vimentin synthesis) .
- Additional changes include the decreased expression function of cell junctional communication proteins (e.g. , E-cadherin, ZO-1), attachment factors (e.g. , integrins), and extracellular matrix proteins (e.g. , thrombospondin) as well as increased proteolytic activity (e.g. , stromelysin, MMPs).
- cell junctional communication proteins e.g. , E-cadherin, ZO-1
- attachment factors e.g. , integrins
- extracellular matrix proteins e.g. thrombospondin
- MMPs extracellular matrix proteins
- a significant proportion of late stage, advanced breast cancers (ABC) are represented in vitro by cultured BC cells that exhibit hormonal independence, decreased intercellular communication and adhesion, enhanced motility, and increased invasiveness through a reconstituted basement membrane (i.e. , matrigel) (Thompson et al , J. Cell Phvsiol. 150:534-544 (1992)).
- GEFs Gene Expression Fingerprints
- Additional GEFs can be designed to substitute for other assays typically used to measure cancer cell progression, such as proliferation (e.g. , proliferative activity), apoptosis (e.g. , apoptotic response), angiogenesis (e.g. , a ⁇ giogenic activity), differentiation, inflammation, and cell-cell or cell-matrix interaction.
- the strategy is to identify genes whose expression is changed in the majority of ABCs and is also modulated during the process of tumorigenesis or tumor/metastasis suppression.
- Genes in the set of common differentially expressed genes whose expression is altered by known anti-invasive or anti-metastatic drugs will be preferentially included in a GEF used for drug screening.
- the GEFs will be diagnostic for ABC and predictive of drug efficacy in the treatment of ABC.
- the alteration of the GEF of the screening cell line(s) identifies a compound as a potential lead for further optimization.
- ER, E-cadherin, and vimentin separates the BC cell lines into three groups [Table 5: group I is ER-positive (ER+), E-cadherin positive (E-cad+), vimentin-negative (Vim-); group II is negative for all markers; group III is negative for ER and E-cadherin expression, but positive for vimentin expression] .
- group I is ER-positive (ER+), E-cadherin positive (E-cad+), vimentin-negative (Vim-); group II is negative for all markers; group III is negative for ER and E-cadherin expression, but positive for vimentin expression
- group III When categorized based upon their invasive ability in the Boy den chamber assay, these BC cell lines are separated into only two groups: a weakly invasive (Inv-w) one (encompassing cell lines in groups I and II) and a highly invasive (Inv-h) one (group III).
- BC cell lines that express vimentin are highly invasive and exhibit a characteristic stellate morphology when cultured in matrigel.
- the cells in this group are the only BC cell lines that are capable of forming metastases to either the lung and lymph nodes (i.e. , MDA231, Hs578T, MDA435) or the brain (i.e. , MDA435) (Price et al , Cancer Res. 50:717-721 (1990)].
- Table 5 Characteristics of Human Mammary Epithelial Cells Employed in this Study
- BP benzopyrene
- PE pleural effusion
- Ca carcinoma
- Tumorigenicity is recorded as + if the cell line has been reported to produce palpable tumors as xenografts in nude athymic or SCID mice.
- the gene expression profiles for all of the BC cell lines that represent different clinical stages and phenotypic states in BC progression have been determined by using cDNA arrays obtained from Clontech (i.e. , Human Atlas I). This analysis can be expanded to include additional genes (e.g. , other arrays, cDNA libraries) and cell sources.
- additional genes e.g. , other arrays, cDNA libraries
- MEC mammary epithelial cell
- RNA from each of the cell lines was isolated and used to prepare a radiolabeled complex cDNA probe for hybridization to the Atlas I arrays.
- These filters contain cDNA fragments corresponding to 588 different genes that represent six functional gene classes, including oncogenes and tumor suppressor genes, genes involved in cell cycle control, cell-cell interactions, apoptosis, and signal transduction pathways. Approximately 300 of the 588 genes were detectable in these analyses indicating that over half of the genes present on the Atlas I array are expressed in human mammary epithelial cells.
- the hybridization signals from each cDNA spot were quantitated and compared with the signals obtained for the same gene in the arrays hybridized with a probe prepared from the reference MCFIOA RNA.
- the values correspond to the number of cell lines in which changes in mRNA level of at least two-fold were observed for the indicated gene.
- 11 were differentially expressed in the majority of the tumor cell lines compared to the reference "normal” control (Table 6).
- the plectin gene was 42 differentially expressed in all 14 BC cell lines, whereas the levels of the B-myb, transferrin R, and ICH-2 protease genes changed in 8 of the 14 cell lines (see Table 6).
- Table 7A shows the fold-differences in mRNA level observed for these genes in each of the cell lines relative to its expression in the reference MCFIOA. The expression of most of the genes (i.e. , 8/11) was decreased in the BC cells relative to "normal" cells.
- the other three genes (i.e. , B-myb, MacMarcks, and transferrin R) showed elevated expression in the BC cell lines.
- Other "normal” cells i.e. , 76N and 184B5
- exhibited minimal alteration in the expression of these genes Figure 3 A and data not shown.
- the pattern of expression changes i.e. , increases or decreases relative to "normal” cells) for these genes represent "tumor- associated" changes found in cultured breast tumor cell lines.
- the number of cell lines with changes in expression of the indicated gene relative to MCF1 OA is provided. Only fold-changes greater than 2 were scored.
- the consensus GEFs for weakly and highly invasive cancers are graphically depicted in Figure 3A.
- the GEF of a normal MEC strain i.e. , 76N
- Three sub-profiles can be distinguished: a tumor-associated GEF comprising 11 genes (Figure 3 A, left-handed striped bars (bars having a stripe angling downward from left to right)), a GEF representative of weakly invasive carcinomas comprising 8 genes ( Figure 3 A, solid bars), and a GEF diagnostic for highly invasive, ABC comprising 6 genes ( Figure 3A, right-handed striped bars (bars having a stripe angling upward from left to right)).
- the other is the HBLIOO cell line that was established from human milk epithelial cells and subsequently shown to contain integrated SN40 genomic sequences that encode the T antigen protein (Vanhamme and Szpire, Carcinogenesis 9:653-655 (1988)).
- the expression profiles of these two cell lines are shown in Figure 3B. From these patterns, we predict that the HBL-100 cell line is a tumor-derived mesenchymal- like, highly invasive cell line; in contrast, the 006FA-2B cells are significantly different from "normal" immortal HMEC such as the MCFIOA and 184B5, but do not exhibit the differential gene expression pattern of either of the tumor cell phenotypes profiled in these studies.
- the growth characteristics in matrigel of these two cell lines were assayed in order to determine whether they demonstrated the morphology associated with the phenotypes predicted by their GEF.
- the 006FA-2B adopted a fused morphology in matrigel whereas the HBL-100 grew with the stellate morphology characteristic of mesenchymal cells with highly invasive ability (data not shown).
- the GEFs identified in cell culture models of breast cancer have value in staging clinical specimens or evaluating responses to drug therapy.
- the gene expression patterns were determined for three tumor biopsies obtained from patients with moderately differentiated infiltrating ductal carcinomas of the breast and compared with the gene expression profile of normal breast tissue.
- the 46 characteristic tumor- associated GEF is found in all three of the tumors, being most pronounced in tumors T8911044 and T8911045. Furthermore, all of these tumors exhibit a GEF that is correlated with weakly invasive tumors. These data indicate that GEFs similar to those described here useful in the diagnosis and treatment of cancer patients. They also suggest that the cultured cells faithfully reproduce some of the gene expression changes observed in the in vivo tumor environment.
- the GEFs identified up to this point are diagnostic of the phenotypic states of highly and weakly invasive cells. These gene expression differences are valuable in diagnostic applications. Also of interest is whether gene expression differences are able or sufficient to report the activity of anti-invasive or metastatic drugs. The selection of a subset of these 28 genes that is most useful in predicting drug efficacy is assisted by determining whether any of these genes are associated with the process of malignant progression. To that end, we measured gene expression changes that occur during cellular transformation as well as tumor and/or metastasis suppression. Models for these processes include oncogene-transformed normal HMEC, tumor suppressor gene-transfected tumor cells, and treatments with anti-neoplastic drugs or differentiating agents.
- EMT e.g. , treatment with anti-E-cadherin antibodies
- EMT can also be employed to define the genes that report the invasive properties of BC cells.
- Information concerning gene expression changes that correlate with the reduction in invasive capacity in response to treatment with drugs or invasion-suppressor gene products is also desirable for deriving the GEF for compound screening.
- HMEC normal limited lifespan HMEC can be immortalized by expression of the SV40 T antigen, the HPV E6 oncogene, or selected p53 mutant proteins (Band, Intl. J. Oncol. 12:499-507 (1998)).
- Atlas I array we measured the gene expression changes that occurred in HMEC immortalized by infection with mutant p53-expressing 47 retrovirus (Gao et al , Cancer Res. 56:3129-3133 (1996)).
- the expression level of 13 genes was affected following immortalization with three different p53 mutant proteins that act as dominant-negative inhibitors of p53 function; notably, 6 of them are included in the "tumor-associated" GEF (Table 8).
- genes that predict anti- invasive drug activity is aided by measuring the gene expression changes resulting from treatment of highly invasive cells with anti-invasive or anti-metastatic drugs. By comparing the effects of anti- invasive compounds that have different known mechanisms of action, a common set of genes whose expression changes report anti-invasive activity can be derived. Also important is the determination of the gene expression changes caused by drugs that are ineffective in blocking invasion, but have other anti-neoplastic properties (e.g. , pro- apoptotic, anti-angiogenic, anti-proliferative), as well as compounds that are modulators of signaling pathways that do not result in the inhibition of invasion.
- anti-neoplastic properties e.g. , pro- apoptotic, anti-angiogenic, anti-proliferative
- Taxol's efficacy is reported to be dependent upon its inhibition of microtubule formation, while mevastatin inhibits HMG CoA reductase and indirectly protein prenylation, thereby leading to cell cycle arrest in the GI phase.
- Sodium butyrate is a differentiating agent that causes histone acetylation and transcriptional activation.
- RA has anti-proliferative and differentiating effects in some BC cell lines (i.e. , ER+), but is ineffective in others (i.e. , ER-negative).
- Taxol and mevastatin are capable of blocking the development of the characteristic stellate mesenchymal cell morphology of MDA231 cells, while sodium butyrate is not effective (data not shown). Taxol has also been shown to prevent invasion of MDA231 in the Boyden chamber assay (Sasaki and Passanti, Biotechniques 24: 1038-1043 (1998)) and mevastatin inhibits 48 mammary tumor metastases in vivo (Alonso et al , Breast Cancer Res. Treat. 50:83-93 (1998)). The highly invasive MDA231 BC cells were treated with these compounds under conditions (i.e. , concentration and time) reported to have maximal effects with little toxicity.
- Taxol, mevastatin, and butyrate treatment caused changes of greater than two-fold in the expression of approximately 10% of the expressed Atlas I array genes (i.e. , taxol: 27/300; mevastatin: 33/300; butyrate: 39/300), while little effect was observed with either RA or CA treatment.
- the gene expression profiles of each of these compounds are readily distinguishable from each other ( Figure 4).
- 12 of the 28 genes identified as potential reporters of either tumorigenicity or stage of invasiveness are modulated by one or more of these drugs.
- the direction of the gene expression change elicited by these drugs for 11 of these 12 genes is towards a more "normal" or less invasive GEF (Table 8).
- GEF that is most predictive of drug efficacy, selectivity for invasive action, and potential toxicity.
- the direction of expression change for each of the indicated genes is tabulated under the Diagnostic heading for differences in BC Cell Lines and Tumor Biopsies relative to MCF10A and normal breast tissue, respectively (data from Tables 7A and 7B and Fig. 3C). Under the Process heading, genes modulated in cells immortalized by p53 inactivation relative to their limited lifespan counterparts are indicated in the Tumorigenesis column.
- the direction of gene expression change in the highly invasive MDA231 cells in response to treatment with either taxol (taxol), mevastatin (mev), or sodium butyrate (buty) is provided in the Anti-cancer drug column. 50
- the studies described here have derived a GEF incorporating the expression of 28 genes that is useful in distinguishing between weakly and highly invasive BC cell lines and tumor biopsies.
- GEF a subset of gene expression changes associated with all BC cell lines and tumors (i. e. , tumor-associated GEF).
- tumor-associated GEF a subset of gene expression changes associated with all BC cell lines and tumors
- two other distinct sub-GEFs define weakly vs. highly invasive cancers.
- tumor progression model systems i.e. , p53 inactivation
- anti-neoplastic drug treatments have identified genes within the 28 that are modulated in the process of tumorigenesis or during the inhibition of invasion.
- the precise GEF that predicts anti-invasive drug efficacy is a change in the expression of a subset of the 28-gene GEF representative of highly invasive cancer cells. That subset is determined by a selection procedure similar to the one used to derive the diagnostic GEFs. Genes commonly affected by drugs or other agents which modulate the invasive phenotype are compared with the diagnostic GEF to derive the common gene expression changes; this produces a GEF predictive of drug efficacy.
- the gene-cell combinations used to create the screen for anti-invasive compounds includes the highly invasive MDA231 cell line and at least two genes from each of the sub-GEFs described above (i.e. , tumor-associated, weakly invasive, and highly invasive). Gene and cell line selection also considers data from drug treatment of the other highly invasive cell lines as well as weakly invasive ones.
- the GEF screen can be carried out in more than one cell line either in mixed or parallel cultures.
- the 76N human MEC strain and the 184B5 benzopyrene-immortalized human MEC line were cultured in DFCI-1 medium (Band and Sager, Proc. Natl. Acad. Sci. U.S.A. 86: 1249-1253 (1989)).
- the 006FA-2B cell line was established from a benign fibroadenoma tissue sample by co-transfecting the cultured organoids with plasmid vectors encoding the HPV16 E6 and E7 oncogenes and a selectable SVneo plasmid using a standard calcium phosphate-mediated procedure.
- 006FA-2B is one of several stable epithelial cell clones with extended lifespan that were selected using G418 (100 ⁇ g/ml, Gibco).
- MCFIOA, HBL-100, T47D, ZR75-1, MCF7, BT483, MDA361, BT474, BT20, MDA468, SKBR3, MDA453, BT549, Hs578T, MDA231 , and MDA435S 51 cells were obtained from the ATCC (Rockville, MD) and initially cultured in the ATCC- recommended medium.
- the cells were cultured to 80-90% confluency in ⁇ -MEM medium [alpha-modified MEM supplemented with 1 mM HEPES, 2 mM glutamine, 0.1 mM MEM non-essential amino acids, 1.0 mM sodium pyruvate, 50 ⁇ g/ml gentamicin, 1.0 ⁇ g/ml insulin (all from Gibco, Gaitherburg, MD), and 10 % FBS (Intergen)].
- ⁇ -MEM medium alpha-modified MEM supplemented with 1 mM HEPES, 2 mM glutamine, 0.1 mM MEM non-essential amino acids, 1.0 mM sodium pyruvate, 50 ⁇ g/ml gentamicin, 1.0 ⁇ g/ml insulin (all from Gibco, Gaitherburg, MD), and 10 % FBS (Intergen)
- ⁇ -MEM medium alpha-modified MEM supplemented with 1 mM HEPES, 2 mM glutamine
- Cells were fed with fresh medium containing 3 mM sodium butyrate (Specialty Media, Inc. Lavallette, NJ), 5.0 ⁇ M taxol (Molecular Probes, Inc. , Eugene, OR), 10 "8 M caffeic acid, 1.0 M retinoic acid, or 20 ⁇ M mevastatin (all from Sigma) and cell monolayers harvested 72 hours (h) later for RNA isolation.
- 3 mM sodium butyrate 3 mM sodium butyrate
- 5.0 ⁇ M taxol Molecular Probes, Inc. , Eugene, OR
- 10 "8 M caffeic acid 1.0 M retinoic acid
- 20 ⁇ M mevastatin all from Sigma
- RNA from cell lines and compound-treated cells was isolated by the guanidinium-isothiocyanate-CsCl gradient procedure (Chirgwin et al , Biochemistry 18: 5294-5299 (1979)).
- Total RNA from normal and tumor tissue specimens was obtained from BioChain Institute, Inc (San Leandro, CA).
- the preparation of radioactively labeled cDNA from total RNA (5 ⁇ g) was performed essentially as described in the Clontech Atlas I cDNA array hybridization kit protocol. The only exceptions were the step for removal of unincorporated nucleotide triphosphate, which was carried out using a G50 spin column and the length of prehybridization, which was increased to at least 6 h.
- the probe concentration routinely employed in the hybridization reactions was 0.7-1.0 x 10 6 counts per minute/milliliter (cpm/ml) .
- ratio thresholds were 2-fold and z score values were 0.3.
Abstract
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JP2000528723A JP2002505852A (en) | 1998-01-26 | 1999-01-25 | Gene expression method for screening compounds |
IL13737199A IL137371A0 (en) | 1998-01-26 | 1999-01-25 | Gene expression methods for screening compounds |
CA002317650A CA2317650A1 (en) | 1998-01-26 | 1999-01-25 | Gene expression methods for screening compounds |
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Cited By (7)
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WO2000022168A1 (en) * | 1998-10-13 | 2000-04-20 | Bioreliance Testing And Development, Inc. | Carcinogen assay |
WO2001061050A2 (en) * | 2000-02-17 | 2001-08-23 | Millennium Pharmaceuticals, Inc. | Methods and compositions for the identification, assessment, prevention and therapy of human cancers |
WO2001075181A2 (en) * | 2000-03-31 | 2001-10-11 | Societe De Conseils De Recherches Et D'applications Scientifiques S.A.S. | Method of identifying ginko biloba in a plant extract by gene profiling |
WO2001077389A2 (en) * | 2000-04-05 | 2001-10-18 | Incyte Genomics, Inc. | Genes expressed in foam cell differentiation |
WO2004005542A2 (en) * | 2002-07-03 | 2004-01-15 | Henkel Kommanditgesellschaft Auf Aktien | Method for identifying infection-specific regulated genes of the skin |
EP1476747A2 (en) * | 2002-01-31 | 2004-11-17 | Gene Logic, Inc. | Molecular hepatotoxicology modeling |
US8014954B2 (en) * | 2005-04-05 | 2011-09-06 | Merck Sharp & Dohme Corp. | Methods for characterizing agonists and partial agonists of target molecules |
Families Citing this family (1)
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CN104975063B (en) * | 2014-04-01 | 2020-04-03 | 埃提斯生物技术(上海)有限公司 | Screening method and application of antitumor drug biomarker |
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US6593084B2 (en) | 1998-10-13 | 2003-07-15 | Robert E. Bird | Carcinogen assay |
WO2001061050A2 (en) * | 2000-02-17 | 2001-08-23 | Millennium Pharmaceuticals, Inc. | Methods and compositions for the identification, assessment, prevention and therapy of human cancers |
WO2001061050A3 (en) * | 2000-02-17 | 2003-02-27 | Millennium Pharm Inc | Methods and compositions for the identification, assessment, prevention and therapy of human cancers |
WO2001075181A2 (en) * | 2000-03-31 | 2001-10-11 | Societe De Conseils De Recherches Et D'applications Scientifiques S.A.S. | Method of identifying ginko biloba in a plant extract by gene profiling |
WO2001075181A3 (en) * | 2000-03-31 | 2002-11-07 | Sod Conseils Rech Applic | Method of identifying ginko biloba in a plant extract by gene profiling |
WO2001077389A3 (en) * | 2000-04-05 | 2003-04-24 | Incyte Genomics Inc | Genes expressed in foam cell differentiation |
WO2001077389A2 (en) * | 2000-04-05 | 2001-10-18 | Incyte Genomics, Inc. | Genes expressed in foam cell differentiation |
EP1476747A2 (en) * | 2002-01-31 | 2004-11-17 | Gene Logic, Inc. | Molecular hepatotoxicology modeling |
EP1476747A4 (en) * | 2002-01-31 | 2008-06-11 | Ocimum Biosolutions Inc | Molecular hepatotoxicology modeling |
WO2004005542A2 (en) * | 2002-07-03 | 2004-01-15 | Henkel Kommanditgesellschaft Auf Aktien | Method for identifying infection-specific regulated genes of the skin |
WO2004005542A3 (en) * | 2002-07-03 | 2004-05-13 | Henkel Kgaa | Method for identifying infection-specific regulated genes of the skin |
US8014954B2 (en) * | 2005-04-05 | 2011-09-06 | Merck Sharp & Dohme Corp. | Methods for characterizing agonists and partial agonists of target molecules |
US8744778B2 (en) | 2005-04-05 | 2014-06-03 | Merck Sharp & Dohme Corp. | Methods for characterizing agonists and partial agonists of target molecules |
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AU2341999A (en) | 1999-08-09 |
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