WO2002082969A2 - Diagnostics and therapeutics for glaucoma, retinal degenerative diseases and cardiovascular diseases based on novel nucleic acids and protein forms of myocilin (myoc) - Google Patents

Diagnostics and therapeutics for glaucoma, retinal degenerative diseases and cardiovascular diseases based on novel nucleic acids and protein forms of myocilin (myoc) Download PDF

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Publication number
WO2002082969A2
WO2002082969A2 PCT/US2001/048622 US0148622W WO02082969A2 WO 2002082969 A2 WO2002082969 A2 WO 2002082969A2 US 0148622 W US0148622 W US 0148622W WO 02082969 A2 WO02082969 A2 WO 02082969A2
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myoc
subject
disease
glaucoma
nucleic acid
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PCT/US2001/048622
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French (fr)
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Tim Hing Kong
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Tim Hing Kong
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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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • MYOC novel nucleic acid and protein forms of MYOC
  • the invention primarily relates to the "fingerprinting of nucleic acids or proteins', that is, the generation of a signature characteristic of the base sequence of a nucleic acid template, or the base sequence of a protein, respectively.
  • Glaucoma Glaucoma
  • Glaucoma is a group of eye diseases, that here in the United States, is the second leading cause of legal blindness, and the leading cause of blindness in African- American individuals.
  • POAG Primary open angle glaucoma
  • JOAG Juvenile open angle glaucoma
  • the gene linked to this form of glaucoma has recently been cloned and identified to be the MYOC gene (Stone et al., 1997), but published research data shows that only about 4% of glaucoma patients have genetic mutations in the gene.
  • the present invention is based, on the recent finding by the inventor (T. H. Kong, unpublished results) that in addition to the wild type (i.e. full length), shorter messenger ribonucleic acids transcripts (e.g.
  • mRNAs with a deletion) of the gene for the Trabecular meshwork Inducible Glucocorticoid Responsive protein (TIGR), also known as the Myocilin protein (MYOC) are expressed in cells of ocular and non-ocular origin of the human body.
  • TIGR Trabecular meshwork Inducible Glucocorticoid Responsive protein
  • MYOC Myocilin protein
  • the invention relates particularly to probes and methods for evaluating MYOC mRNA species that are differentially expressed in diseased compared to normal individuals.
  • Retinal degenerative diseases are disorders that lead to the degeneration of the retina. Degeneration of the retina impairs the ability to see, leading to legal, if not complete blindness. Over 6 million Americans are losing sight to one of these diseases.
  • RP Retinitis Pigmentosa
  • MD Macular degeneration
  • Usher Syndrome Retinitis Pigmentosa
  • the present invention is based, on the recent finding by the inventor (T. H. Kong, unpublished results) that in addition to the wild type (i.e. full length), shorter messenger ribonucleic acids transcripts (e.g. mRNAs with a deletion) of the gene for the Trabecular meshwork Inducible Glucocorticoid Responsive protein (TIGR), also known as the Myocilin protein (MYOC), are expressed in cells of ocular and non-ocular origin of the human body. In addition, from studies on ocular tissues, these shorter mRNAs have shown to be differentially expressed in normal and retinal diseased individuals. Methodologies described by the current invention can be used for the prognosis/diagnosis of people with RDD whether they are asymptomatic or have clinical symptoms, at any stage of the disease.
  • TIGR Trabecular meshwork Inducible Glucocorticoid Responsive protein
  • MYOC Myocilin protein
  • the invention relates particularly to probes and methods for evaluating the presence of MYOC mRNA species that are differentially expressed in retina diseased subjects compared to normal subjects.
  • Cardiovascular diseases result from pathological processes affecting either, the heart- muscle (myocardium), its lining membrane (endocardium), or its outer covering and enclosing sac (pericardium).
  • TIGR Trabecular meshwork Inducible Glucocorticoid Responsive protein
  • MYOC Myocilin
  • mRNAs with a deletion) of the gene for the Trabecular meshwork Inducible Glucocorticoid Responsive protein also known as the Myocilin protein (MYOC) are expressed in cells of ocular and non-ocular origin of the human body.
  • TIGR Trabecular meshwork Inducible Glucocorticoid Responsive protein
  • MYOC Myocilin protein
  • the shorter MYOC mRNA species have been detected also.
  • the inventor has demonstrated that the wild type and novel (i.e. shorter) forms of the MYOC mRNA are differentially expressed in normal and diseased individuals in other tissues, in relation to other genetic disorders.
  • Methodologies described by the current invention can be used for the prognosis/diagnosis of people with cardiovascular diseases whether they are asymptomatic or have clinical symptoms, at any stage of the disease. Genetic probes and methods of use thereof in the prognosis/diagnosis of cardiovascular disease are described herein.
  • the invention relates particularly to probes and methods for evaluating the presence of MYOC mRNA species that are differentially expressed in diseased individuals compared to normal individuals.
  • the invention includes a variety of methodologies for generating genetic profiles or 'fingerprints' for prognostic and diagnostic use.
  • methodologies for the making of microarrays of biological macromolecules for example, microarrays of nucleic acid molecules or proteins
  • the use of microarrays to generate genetic 'fingerprints' do not rely on the rate- limiting step of gel electrophoresis, and can therefore, produce a large number of genetic profiles in a short time.
  • the term "disease(s)” refers to a Glaucoma disease, or to a Retinal Degenerative disease, or to a cardiovascular disease.
  • the terms "Glaucoma” or “Glaucoma disease” refers to a collection of different eye diseases that are characterized by a specific pattern of damage to the optic nerve, and a loss in the visual field.
  • the terms includes the various types of glaucoma, including Primary open angle glaucoma, juvenile open angle glaucoma, normal tension glaucoma, angle closure glaucoma, acute glaucoma, pigmentary glaucoma, etc. Most types, but not all, are associated with an elevation in the intraocular pressure. This is not the disease itself, but a major risk factor in the development of glaucoma.
  • RDD spinal degenerative diseases
  • Age Related Macular Degeneration Retinitis Pigmentosa, Usher Syndrome, Stargardt Disease, Bardet-Biedl Syndrome, Best Disease, Choroideremia, Juvenile Retinoschisis, Leber Congenital Amaurosis, Blue-Cone Monochromacy, Central Areolar Choroidal Dystrophy, Cone-Rod Dystrophy, Cone Dystrophy, Congenital Stationary Night Blindness, Dominant Drusen, Goldmann-Favre Dystrophy, Gyrate Atrophy, Kearns- Sayre Syndrome, Macular Drusen, Macular Dystrophy, Malattia Leventinese, Oguchi Disease, Refsum Disease, Atypical RP, Retinitis Punctata Albescens, Rod Dystrophy, Rod-Cone Dystrophy, Rod Monchromatism, Sector RP, Sor
  • cardiovascular diseases refers to all cardiovascular diseases and the following is not intended to be an exhaustive list:
  • Congenital heart diseases for example, Patent ductus arteriosus, Pulmonary stenosis,
  • Aortic stenosis Coarctation of the aorta, Bicuspid aortic valve, Subaortic stenosis,
  • myocardium for example, Acute myocardium, chronic myocardium, Myocardial ischaemia, etc.
  • Stroke for example, cerebral thrombosis, cerebral embolism etc.
  • Endocardium for example, Acute endocarditis, rheumatic heart disease, etc.
  • Hypertensive heart diseases any cardiac diseases having an elevated blood pressure component.
  • Arteriosclerotic heart diseases any coronary diseases involving the thickening or hardening of the arteries.
  • Diseases affecting the pericardium for example, Pericarditis, etc.
  • Cardias for example, Arrhythmias, tachycardia, bradycardia, ventricular tachycardia, ventricular fibrillation, atrial fibrillation etc.
  • cardiac rhythm for example, Arrhythmias, tachycardia, bradycardia, ventricular tachycardia, ventricular fibrillation, atrial fibrillation etc.
  • Heart-block any disease or degeneration of the 'pacemaker' causing partial or complete arrest of the impulses governing the heart beat).
  • nucleic acids refers to oligonucleotides (for example, when referring to primers or probes) or polynucleotides (for example, when referring to probes, DNA fragments, genes) of deoxyribonucleic acid (DNA) or, where appropriate, ribonucleic acid (RNA). It is also understood to include nucleotide analogs of DNA or RNA, and the nucleic acids may be single (sense or antisense) or double-stranded.
  • MYOC nucleic acid refers to a nucleic acid encoding an MYOC polypeptide, such as nucleic acids having SEQ ID NOS. 1 or 3, as well as fragments thereof, complements thereof, and derivatives thereof, and is intended to include the novel deleted and truncated forms, of figure 4 and any other naturally occurring shorter forms.
  • protein protein
  • polypeptide polypeptide
  • peptide protein
  • MYOC polypeptide and “MYOC protein”
  • allele and “allelic variant”, used interchangeably herein, refers to different forms of a gene or portions thereof.
  • allelic variants of a gene can differ from each other by a single nucleotide, or more. They include differences arising from a deletion, an insertion, a substitution, a rearrangement, (i.e. differences arising from a mutational event). Alleles of the same gene occupy the same position or locus on homologous chromosomes. A subject having two identical alleles of a gene, is said to be homozygous for the gene or allele. On the other hand, if the subject has two different alleles for the gene, the subject is said to be heterozygous for that gene.
  • the term "allelic variant of a polymorphic region of a MYOC gene” or words to that effect refers to a region of a MYOC gene having one or several nucleotide sequences found in that region of the gene in other individuals.
  • wild type allele refers to an allele or form of a gene which when present in both copies will result in a subject having the wild type phenotype. As some nucleotide sequence changes may not result in amino acid changes, and furthermore, as some amino acid changes may not result in a change of the phenotype, there can be several different or alternative forms of the wild type allele for a specific gene.
  • antagonist refers to an agent or compound which can downregulate (for example, suppresses or inhibits) one or more of MYOC bioactivities. This could occur by downregulating the expression of a MYOC gene or by reducing the amount of MYOC protein present. It could also occur by inhibiting or decreasing the interaction between a MYOC protein and another molecule, for example, an upstream region of a gene, which is regulated by a MYOC transcription factor.
  • the MYOC antagonist can be a MYOC antisense nucleic acid, or a nucleic acid encoding a dominant negative form of a MYOC polypeptide, or it can be a ribozyme which can interact specifically with a MYOC RNA.
  • Further MYOC antagonists can be peptides, antibodies and small molecules, which is capable of binding to a MYOC polypeptide and inhibiting its action.
  • the term "Agonist” refers to an agent or compound which can upregulate (for example, supplements or potentiates) one or more of MYOC bioactivities. This could occur by upregulating the expression of a MYOC gene or by increasing the amount of MYOC protein present. It could occur by enhancing or increasing the interaction between a MYOC protein and another molecule, for example, an upstream region of a gene, which is regulated by a MYOC transcription factor.
  • the MYOC agonist can be peptides, antibodies and small molecules, which is capable of binding to a MYOC polypeptide and enhancing its action.
  • activity has the same meaning as “ Bioactivity”, or "Biological activity” or “biological function”, and refers to the effector or antigenic function performed directly or indirectly by a MYOC polypeptide (either native or denatured form), or by any parts thereof.
  • the biological activities include binding to a target nucleic acid (for example, an upstream region of a gene, which is regulated by a MYOC transcription factor), and a MYOC bioactivity can be altered by directly affecting an MYOC polypeptide, or by changing the level of a MYOC polypeptide (e.g. by modulating the expression of a MYOC gene).
  • sequences has the same meaning as “Similarity”, or “Homology”, and refers to the degree of similarity between two or more polypeptide sequences, or between two or more nucleic acid sequences.
  • the sequences may be aligned and compared with respect to a particular position in the sequence. If the same amino acid or base is found at the position, then the sequences are said to be identical at that position. The sum of all the identical matches throughout the aligning sequences is then a measure of the degree of similarity between them.
  • a sequence "unrelated" to the subject myocilin sequences of the invention will share less than 38% sequence identity with them, preferably less than 24% sequence identity.
  • the terms "cells”, or “host cells”, shall have the same meaning and is understood to refer not only to the particular subject cells, but also within the scope of the terms, to the progeny or potential progeny of the subject cells. It is also understood that the cells may undergo mutational events or subjected to environmental influences and therefore the progeny cells may not be identical to the subject cells from which they are derived.
  • nucleic acid strand can refer to the complement of a coding strand or the complement of a non-coding strand. Therefore, the term “nucleotide sequence complementary to the nucleic acid set forth in SEQ ID No. x" refers to the nucleic acid that is the complementary strand to the nucleic acid strand set forth in SEQ ID No. x. The nucleotide sequences and the complementary nucleotide sequences are always given in the 5' to 3' direction.
  • a gene may have one or more copies in the genome. Where there are multiple copies, each copy may differ in the nucleotide sequence, due to deletions, insertions, rearrangements etc., but which may encode essentially the same polypeptide with substantially the same activity. Therefore, the term "DNA sequence encoding a MYOC polypeptide", or words to that effect, is meant to refer to all the MYOC genes in an individual. Differences in sequences due to allelic differences between individuals are also understood to be within the scope of the term.
  • MYOC therapeutics refers to various MYOC polypeptide forms, nucleic acids, peptidomimetics, or any small molecules, which are able to alter or modulate one or more activities of a wild type MYOC protein or that of the MYOC protein binding partner (MPBP).
  • MYOC therapeutic which is able to mimic, potentiate, or upregulate one or more activities of a wild type MYOC protein or the MPBP is a "MYOC agonist”.
  • a MYOC therapeutic which is able to inhibit, suppress, or downregulate one or more activities of a wild type MYOC protein or the MPBP is a "MYOC antagonist".
  • the term “interact” refers to any detectable associations between molecules, preferably biochemical associatons. It is understood to include interactions of protein-protein, protein-nucleic acid, nucleic acid-nucleic acid, protein-small molecules, nucleic acid-small molecules.
  • sample as used in the context "...a sample obtained from a subject" as used herein, is meant to refer to tissues, cells, or bodily fluids (for example Aqueous humor, Vitreous humor, tears, blood, saliva, urine etc.) either of an ocular or non-ocular origin.
  • nucleic acids i.e. DNA and RNA
  • isolated refers to nucleic acids encoding a MYOC polypeptide that is separated from other DNAs and RNAs that are naturally or orginally present in the source.
  • An isolated MYOC nucleic acid usually has less than 8 kilobases of flanking sequences, and preferably less than 2 kilobases of flanking sequences, on either side of the gene.
  • polypeptides refers to MYOC polypeptides, either recombinant or purified, that are separated from other cellular proteins, nucleic acids, and small molecules.
  • mutation refers to alterations to the nucleotide sequence of a gene, or the amino acid sequence of the gene product.
  • the term includes deletions, insertions, rearrangements, or single base or amino acid substitutions.
  • MYOC mutations that are likely to contribute or cause the disease can occur at the DNA level (genomic mutations) or at the transcript level. At the mRNA level, the term includes the shorter MYOC forms, documented in figure 4 and any other naturally occurring shorter forms.
  • mutated gene or “mutated allele”, as used herein, refers to the allelic forms of the gene (i.e. not wild type) that are capable of altering the phenotype of the individual (for example, normal state to disease state).
  • non-human animals is intended to refer to the following list, not intended to be exhaustive; chickens, cow, dog, sheep, non-human primates, amphibians, reptiles, etc., preferably to rodents (e.g. rats) and more preferably, to mice.
  • rodents e.g. rats
  • Transgenic or chimeric animals refers to animals, which harbors the recombinant gene, or the transgene, or the heterologous gene, or animals expressing such a gene, or animals where such a gene is expressed in some cells but not in others.
  • polymorphism refers to the coexistence of two or more forms (i.e. two or more different sequences) of a gene (e.g. allelic variant) or part thereof, within an individual or between individuals.
  • the polymorphism may arise due to a single nucleotide difference (as in SNP polymorphism) or can be several nucleotides or more long
  • a "polymorphic gene” is a gene which has one or more polymorphic region (i.e. a region exhibiting polymorphism).
  • promoter refers to a DNA sequence that regulates expression of a specific DNA sequence that is operatively linked to it.
  • the term includes “constitutive promoters” (i.e. requires no induction for expression), and “inducible promoters” (i.e. expression can be controlled).
  • the term also includes “leaky promoters” (i.e. expression takes place primarily, but not exclusively, in certain cells, or under certain conditions) and "tissue-specific promoters” (i.e. can regulate expression in specific cells of a tissue or tissues, and no others).
  • small molecule refers to nucleic acids, peptides, polypeptides, peptidomimetics, lipids, carbohydrates, organic (i.e. carbon containing) or inorganic entities, having a molecular weight of less than 6 kilodaltons (kD), preferably less than 5 kD, and more preferably less than 4 kD.
  • kD kilodaltons
  • Many companies e.g. pharmaceutical companies
  • have extensive libraries of small molecules of various origins e.g. chemical, bacterial, fungal, etc
  • support as used herein and in the context of hybridization or interacting molecules, shall include but not limited to, a porous or non-porous membrane, a polyacrylamide layer, a substrate, a glass or microscope slide, etc..
  • the term “specifically hybridizes”, as used herein, is meant to refer to the ability of a nucleic acid molecule of the current invention to hybridize or bind to a target molecule of at least approximately 7, 14, 21, 28, 50, 100, 150, 200, 300, 350, 400, 450 or 500 consecutive nucleotides.
  • the target molecule is a vertebrate gene, more preferably a MYOC gene.
  • an array/microarray of "distinct polynucleotides” means an array/microarray containing, as its members, (1) polynucleotides of different sequences, and/or (2) polynucleotides differing in amount or concentration, or (3) polynucleotides of different mixtures of two or more distinct members.
  • Cell type means a cell from a given source.
  • This given source can be, for instance, a tissue, or organ, or a cell with a given pathology or genetic makeup, or a cell in a given state of differentiation.
  • An “array” is a linear or two-dimensional array of preferably discrete regions, each possessing a finite area and formed on a solid support surface.
  • a “microarray” is an array of preferably discrete regions, possessing a density of discrete regions of 10/cm 2 or greater, and preferably at 50/cm or greater, more preferably 250/cm or greater.
  • the regions in a microarray have typical dimensions, for instance diameters in the range of about 8 to 300 ⁇ m, and are separated from each other in the array by about the same.
  • Ligand refers to one member in a ligand/anti-ligand pair, and include for instance, an effector molecule in an receptor/effector binding pair; one of the nucleic acid strands in a complementary, hybridized nucleic acid duplex binding pair; or an antibody/antigen or antibody fragment/antigen binding pair.
  • Anti-ligand refers to the opposite member in the above-mentioned pairs of molecules.
  • An “analyte” refers to a macromolecule, for instance a polynucleotide or polypeptide, or antibody whose presence, identity, and/or amount is to be determined. The analyte is a member of a ligand/anti-ligand pair. Preferably, the analyte are the molecules of the current invention.
  • transcriptional profile refers to the expression or the presence of all transcripts of MYOC (i.e. pattern of expression) and their levels of expression. Thus, this is both a qualitative and quantitative profile of MYOC expression at the transcript level.
  • transcriptional profile refers to the expression or the presence of all polypeptides of MYOC (i.e. pattern of expression) and their levels of expression. Thus, this is both a qualitative and quantitative profile of MYOC expression at the protein level.
  • Figure 1 is the cDNA sequence of the human MYOC gene, including the 5' and 3' untranslated region (UTRs) (SEQ ID No.l).
  • Figure 2 is the 1512 base pair Open reading frame (ORF) of the human MYOC gene, provided herein as SEQ ID No.3.
  • Figure 3 is the 504 amino acid sequence of the human MYOC protein, provided herein as
  • Figures 4a, 4b and 4c are figures depicting and listing some of the deleted MYOC cDNAs that has been identified and characterized.
  • Myocilin is also known as the Trabecular meshwork Inducible Glucocorticoid Responsive protein (TIGR)].
  • MYOC is known to be expressed - isolate tissues, cells or bodily fluids (for example Aqueous humor, Viteous humor, tears, blood, urine etc.).
  • MYOC cDNAs by the polymerase chain reaction (PCR) using MYOC specific primers (pair, forward and reverse) whose DNA sequences are derived either from the coding [i.e. Open reading frame (ORF)] or from the non- coding regions (for example, 5'-untranslated, promoter, 3'-untranslated) of the MYOC gene, with any thermostable DNA polymerase or related enzymes (e.g. Taq).
  • ORF Open reading frame
  • the separation medium of 1.5 e.g. agarose gel
  • a solid support for example, nitrocellulose, nylon membranes.
  • the separation medium of 1.5 e.g. agarose gel
  • the position of the bands, the number of bands, the intensity (or color, where a colorimetric or fluorescent label is used) of each individual bands] may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have the disease. Prior calibration of this methodology with known disease and non-diseased subjects is required.
  • the mRNAs are separated as described in 1.5 but under denaturating condition (for example, in formaldehyde-gel based systems). 1.6 is modified to the
  • MYOC Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or bodily fluids (for example Aqueous humor, Viteous humor, tears, blood, urine etc.).
  • the separation medium of 2.3 e.g. polyacrylamide gel
  • the separation medium of 2.3 may be dried and used directly for hybridization.
  • the genetic profile i.e. the translational profile
  • derived from 2.6 i.e. the "barcodes' or the 'fingerprint'
  • a control i.e. non- diseased individual
  • the information provided by the genetic profile i.e. the position of the bands, the number of bands, the intensity (or color, where a colorimetric or fluorescent label is used) of each individual bands] may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have the disease. Prior calibration of this methodology with known diseased and non-diseased subjects is required.
  • An variation of the methodology in (2) uses the principle of immunoprecipitation (IP).
  • IP immunoprecipitation
  • the isolated proteins are mixed and incubated with the MYOC specific antibodies. Proteins, which are not bound to the anti-MYOC antibodies are then removed (for example, using protein A). This is followed by separation (for example, by gel-based electrophoresis) of the MYOC proteins. Then steps 2.5, 2.6 and 2.7 as above.
  • Hybridization to high density oligonucleotide arrays to detect expression of MYOC This invention provides methods for the characterization of the pattern of expression of a multiplicity of MYOC nucleic acid forms, and their expression levels. The methods involve obtaining a sample from a subject, hybridizing the nucleic acids (either mRNAs or the cDNAs derived from it) from the sample to a high density array of oligonucleotide probes (representing naturally occurring MYOC nucleic acid forms) where the high density array contains nucleic acid probes complementary to sequences or subsequences of target nucleic acids in the said nucleic acid sample.
  • the method involves providing a pool of target nucleic acids (derived from a sample obtained from the subject) comprising one or more target mRNA transcripts, or nucleic acids derived from the mRNA transcripts, hybridizing said pool of nucleic acids to an array of said nucleic acid probes immobilized on surface (for example, glass, nylon etc.) where the array comprises more than 50, preferably more than 500, more preferably more than 5000, different nucleic acid probes and each different nucleic acid probe is localized in a predetermined region on the surface of the solid support microarray, the density of the different nucleic acid probes is greater than about 10, preferably greater than 50, more preferably greater than 250 per 1 cm 2 , and the nucleic acid probes are complementary to the RNA transcripts (or nucleic acids derived from the RNA transcripts); qualifying and quantifying the hybridized nucleic acids in the microarray.
  • the said pool of target nucleic acids is radioactively labeled. Other methods of detection may also be used (
  • nucleic acids e.g. DNA fragments
  • the 'library' of cDNA clones i.e. the plasmid nucleic acid of each clone, or just the insert nucleic acid of each clone
  • a solid support for example glass, nylon membrane
  • spotting, or 'printing' or other techniques well known in the art followed by the immobilization of the cDNAs on the support.
  • the cDNA microarrays (identical copies of the microarray having being made in 3.2) are hybridized with single stranded cDNA probes that are derived from the mRNA isolated from the individual under investigation (as outlined in 1.1 to 1.3).
  • the probes are radioactively labeled, and the signals are visualized by autoradiography, but other detection methods may also be used (i.e. non-radioactive labels, such as fluorescent labels or enzymatic labels).
  • the hybridization and the subsequent washing steps are performed to provide a high level of stringency so that incompletely hybridized probes will be unstable and will not give rise to a detectable signal. Thus, a nucleic acid probe hybridizing with a non- identical nucleic acid on the microarray will not result in a hybrid or duplex formation.
  • the resulting pattern and level of hybridization may then be compared to the pattern profile from a control (i.e. non-diseased individual).
  • the information provided by the pattern profile i.e. the location of the 'dots', the number of dots, the intensity (or color in the case of a fluorescent or colorimetric label) of each individual 'dots'] may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have the disease. Prior calibration of this methodology with known diseased and non-diseased subjects is required.
  • a variation of the cDNA microarray is the polypeptide microarray to detect protein expression.
  • epitope-specific antibodies of myocilin are immobilized on the microarray, and hybridized or interacted with the pool of target, labeled polypeptides, derived from the individual under investigation.
  • the resulting translational profile is then analysed as for the transcriptional profile in 3.5 above; used in a statistical calculation to determine the probability that the individual under investigation may or may not have the disease. Prior calibration of this methodology with known diseased and non-diseased subjects is required. Terms and terminology used in conjunction with the invention are known in the art.
  • the invention includes methodologies for forming an array, preferably a microarray, of analyte-assay regions on a solid support, where each region has a known amount of a selected, analyte-specific reagent.
  • the methodologies may be used in forming a multitude of such arrays or microarrays.
  • the invention includes a solid support with a surface (for instance, a glass surface, nylon, etc.) having an array of 10 or more, preferably 50 or more, preferably 250 or more, distinct polynucleotide (single-stranded) or polypeptide biopolymers per cm 2 surface area.
  • Each distinct biopolymer (a) is positioned at a separate, defined location in said microarray, (b) has a length of 10 or more monomer units, preferably 30 or more monomer units, more preferably 90 or more monomer units, and (iii) is disposed in a defined amount in the range of about 0.1 femtomoles to 200 nanomoles.
  • the biopolymers are macromolecules, either MYOC nucleic acids or proteins, and are from a vertebrate.
  • the biopolymers are either MYOC nucleic acids or proteins, and are from a mammal, for example a human.
  • the biopolymers are either MYOC nucleic acids or polypeptides, and has the sequence set forth in SEQ ID No. 1, 2, 3, or figure 4, or a complement thereof (if nucleic acids), or a portion thereof.
  • PCR-based methodologies are used to amplify the wild type and shorter MYOC nucleic acids from cells that originated from a human subject. These amplified MYOC fragments are then converted into single-stranded polynucleotides for fabrication onto a microarray.
  • the MYOC nucleic acids are converted into polynucleotides by isolating the individual amplified fragments from a mixture of fragments in a PCR-based amplification product, followed by the immobilization of these isolated fragments (or clones, or subclones thereof) onto a microarray by means well known to a skill artisan.
  • the invention includes a wide variety of methodologies for the fabrication of ordered microarrays of macromolecules on a surface of a support.
  • the term "support” shall include but not limited to, a porous or non-porous membrane, a polyacrylamide layer, a substrate, a glass or microscope slide, etc.
  • a porous or non-porous membrane a polyacrylamide layer
  • substrate a substrate
  • a glass or microscope slide etc.
  • One methodology is the use of the "dot blot" approach where the nucleic acid is immobilized on the porous membrane by baking the membrane or exposing it to UV radiation.
  • Another methodology utilizes an array of pins dipped into the wells (for instance, the 96 wells of a microtitre plate) for transferring an array of samples to a support.
  • the array may be made employing pins that are designed to spot a surface of the support in a staggered manner (Lehrach, et al., 1990).
  • An ordered microarray of nucleic acids may also be made using elaborate synthetic schemes to synthesize different nucleic acid sequences at different discreet regions of a support [e.g. Pirrung, et. al. (1992), and Fodor, et.
  • the current invention includes technologies for performing nucleic acid hybridization to the above, fabricated microarrays [for example, by sealing the support in a plastic bag (Maniatas, et. al. (1989) or a rotating (e.g. glass) cylinder (Robbins Scientific) with the labeled hybridization probe inside the sealed container].
  • a plastic bag Maniatas, et. al. (1989) or a rotating (e.g. glass) cylinder (Robbins Scientific) with the labeled hybridization probe inside the sealed container.
  • a rotating (e.g. glass) cylinder Robots Scientific
  • the invention also includes methodologies for printing antibodies onto microarrays for screening MYOC polypeptides. For instance, Abouzied, et. al. (1994) devised a method of printing horizontal lines of antibodies on a nitrocellulose membrane and separating areas of the membrane with vertical hydrophobic stripes of material. A variation of this methodology prints MYOC polypeptides onto microarrays (as used herein, an antibody may be a polypeptide, but a polypeptide may not necessarily be an antibody) . Also within the scope of the invention, is the use of these antibody/polypeptide microarrays for the diagnostic and screening applications outlined in the specification.
  • One embodiment of the invention is a methodology for assaying and detecting the differential expression of each of a plurality of MYOC polynucleotides in a first cell type, with respect to expression of the same polynucleotides in a second cell type.
  • the two cell types could represent cells from two different subjects (for instance, a normal subject and a diseased subject), or representing cells derived from two different tissues from the same individual, or representing samples of the same tissue taken at different times of the same individual.
  • fluorescent-labeled other detectable labels may also be used
  • cDNAs derived from mRNAs isolated from the two cell types is first produced, where the cDNAs from the first and second cell types are labeled with first and second different fluorescent reporters, respectively.
  • a mixture of the labeled cDNAs from the two cell types is added to the microarray of polynucleotides representing a plurality of MYOC sequences derived from the two cell types, under conditions that allows the hybridization of the cDNAs to the complementary, immobilized polynucleotides in the microarray. Fluorescence examination of the microarray under excitation conditions in which (a) polynucleotides of the microarray that hybridized predominantly to cDNAs from one of the first or second cell types give a distinct first or second fluorescence emission color, respectively, and (b) polynucleotides hybridized to approximately equal numbers of cDNAs from the first and second cell types give a distinct combined fluorescence emission color, respectively.
  • each MYOC sequence in the two cell types can then be measured by the observed fluorescence emission color of each region in the mircoarray.
  • a variation of the above methodology employs one identical microarray for each cell type studied. In performing the methodology, radioactively labeled (other detectable labels may also be used, for instance enzymatic labels) cDNAs derived from mRNAs isolated from the first cell type is first produced. The mixture of labeled cDNAs is then added to the polynucleotides immobilized on the microarray, under conditions, which will allow hybridization of the cDNAs to the complementary polynucleotides of the microarray.
  • a microarray containing multiple polynucleotide forms of MYOC can be probed with a labeled mixture of a patient's cDNAs (derived from the isolated mRNAs), which will specifically hybridizes with those complementary immobilized single-stranded polynucleotides on the microarray.
  • a labeled mixture of a patient's cDNAs derived from the isolated mRNAs
  • the detection of these interactions can lead to medical prognosis and/or diagnosis with respect to Glaucoma, Retinal degenerative diseases and cardiovascular diseases.
  • Other molecules of genetic interest, such as RNAs can be immobilized on the microarray or alternately used as the labeled probe mixture that is applied to the microarray.
  • total cDNA derived from a normal cell is labeled with one color fluorophore and total cDNA derived from a diseased cell (from sample of diseased subject) with another color fluorophoere and simultaneously hybridizing the two cDNA populations to the same microarray of cDNA polynucleotides allows for differential gene expression to be measured as the ratio of the two fluorophore intensities.
  • This two-color experiment can be used to monitor gene expression in different disease states, tissue types, response to drugs, or response to other treatments/therapies.
  • Such a procedure can be employed to screen many patients or individuals against all known forms or mutations of the MYOC gene.
  • the assay format can be reversed where the patient nucleic acids is immobilized as the microarray elements and each microarray is hybridized with a different mutated allele, or genetic forms.
  • microarrays of whole cells, peptides, enzymes, antibodies, antigens, receptors, ligands, phospholipids, polymers, drug cogener preparations or chemical substances can be fabricated by the means described in the invention for large scale screening assays in medical diagnostics, drug discovery, toxicology and molecular biology.
  • microarrays for performing mass screening for diagnostic applications.
  • numerous microarrays can be fabricated on the same solid support and each microarray reacted with a different population of nucleic acid or polypeptide (in the case of the polypeptide microarrays) probe while the solid support is processed as a single sheet of material.
  • the invention provides screening assays such as cell-free assays, cell-based assays and transgenic animals, for the purpose of identifying therapeutics that are useful in the treatment of the disease or for the prevention of the disease.
  • Cell-free assays can be used to identify MYOC therapeutics which can interact with a MYOC protein, or a MYOC protein binding partner (MPBP), and/or which can modify one or more activities of a MYOC protein or a MPBP.
  • MYOC protein or a MYOC protein binding partner (MPBP)
  • MPBP MYOC protein binding partner
  • An illustrative cell-free assay includes the steps of (i) forming a reaction mixture of (a) a MYOC protein or a functional fragment thereof, (b) a MPBP or a functional fragment thereof (c) a test compound or a library of test compounds, and (ii) detecting the interaction of the molecules in the assay and/or (iii) detecting the alteration in one or more activities of the MYOC protein (or a functional fragment thereof) or the MPBP (or a functional fragment thereof).
  • the detection of interacting molecules i.e. complex formation), the quantitation of a modulation of the complex formation, or the quantitation of one or more activities of the interacting molecules (i.e.
  • the protein to be detected in the complex can be "epitope tagged" in the form of a fusion protein (e.g. a GST-fusion protein).
  • the MYOC protein or its binding partner is immobilized on a support matrix (e.g. by conjugation to biotin or streptavidin) to aid in the separation of the complexes from the uncomplexed molecules, and to enable automation of the assay.
  • the invention also provides cell-based assays for identifying small molecule therapeutics of myocilin which may be an agonist or antagonist.
  • Cell-based assays can be used to identify compounds, which can alter or modulate the expression of the MYOC gene, modulate the translation of one or more MYOC mRNA species, or alter the stability of one or more MYOC mRNA species or polypeptides.
  • a test compound is added to cells capable of expressing the MYOC gene, and the presence of one or more mRNA species or polypeptide is then determined and quantitated (e.g. released of protein into cell medium), and compared to that of control cells not exposed to the test compound.
  • the specificity of the test compound for MYOC can be confirmed by analyzing the expression of one or more control genes (e.g. ⁇ -actin gene).
  • the effect of the test compound on the expression of the MYOC gene at the transcriptional level can be determined with the use of a reporter construct whereby the promoter (or a portion thereof) of the MYOC gene is operatively linked to a reporter sequence, whose gene product can be readily quantifiable (e.g. ⁇ - galactosidase, or luciferase).
  • a reporter construct whereby the promoter (or a portion thereof) of the MYOC gene is operatively linked to a reporter sequence, whose gene product can be readily quantifiable (e.g. ⁇ - galactosidase, or luciferase).
  • a reporter sequence whose gene product can be readily quantifiable (e.g. ⁇ - galactosidase, or luciferase).
  • the invention provides for transgenic non-human animals, which can be used for a number of purposes, and the following is not meant to be an exhaustive list: a) To identify MYOC therapeutics b) Using "knock-out" transgenic animals to determine the function of MYOC, the phenotype of a MYOC knock-out animal, and to identify genes which affect the animal's susceptibility to the disease. c) Using transgenic animals harboring a MYOC promoter/reporter gene transgenic construct to identify compounds, which alter or modulate MYOC expression. d) To screen for drugs that alleviate or attenuate the disease or symptoms of the disease.
  • Transgenic animals of the invention include those harboring a heterologous MYOC gene or fragment thereof, or a reporter gene, under the control of the MYOC promoter or a heterologous promoter. It also includes animals whose endogenous MYOC gene has been "knock-out" (i.e. an animal carrying a heterozygous or homozygous deletion of the MYOC gene).
  • knock-in constructs will contain the necessary sequences required for homologous recombination, a positive selectable marker, but NO omission of the coding sequences.
  • the knock-out and knock-in constructs are flanked by negative selectable markers at either end (e.g. through the use of two allelic variants of the thymidine kinase gene, and incorporating a drug like 5-bromodeoxyuridine into the culture medium).
  • transgenic or knock-out animals are well known in the art.
  • gene targeting in embryonic stem cells can be performed with a transgenic construct designed to undergo homologous recombination with the corresponding genomic sequences, which provides a positive selection trait (e.g. neomycin resistance) in the process.
  • a positive selection trait e.g. neomycin resistance
  • either the FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al. (1991) Science, 251, 1351-1355) or the cre/loxP recombinase system of bacteriophage PI (e.g. see Orban et al.
  • PNAS 89, 6232-6236 can be used to create in vivo site-specific genetic recombination systems.
  • the required ES cells are generated and maintained using methods well known to the skilled artisan (for example, see Doetschman et al. (1985) J. Embryol. Exp. 87, 27-45).
  • suitable ES cells containing the transgene/transgenic construct in the correct location can be identified by the selection techniques described above, the cells can be inserted into the embryo using techniques well known to the skilled artisan (e.g. electroporation, lipofection), preferably by microinjection.
  • the offspring of the foster mother can be screened using a number of methodologies available.
  • they may be screened using Southern blot or PCR (using for example, DNA extracted from tail tissue), or screened for mosaic coat color (if the coat selection strategy is used), or by Northern blots (looking for expression of the gene knocked out or the marker gene or both), or by Western blots (using antibodies directed at the transgene or marker gene's translation product).
  • Southern blot or PCR using for example, DNA extracted from tail tissue
  • screened for mosaic coat color if the coat selection strategy is used
  • Northern blots looking for expression of the gene knocked out or the marker gene or both
  • Western blots using antibodies directed at the transgene or marker gene's translation product.
  • the transgene can be the wild type form of the protein, or variants thereof, or portion thereof, or homologs thereof, agonists or antagonists thereof, or antisense constructs thereof.
  • the expression of the transgene is restricted to certain cells, tissues or developmental stages of the animal, using for example, cis-acting elements that controls the expression in the pattern desired.
  • Generating and analyzing the transcriptional and translational profiles of myocilin may identify therapeutics for the treatment of the disease.
  • the screening assays to identify drug candidates will comprise the following steps:
  • the above screening assays may be adapted for the use of pharmacogenomics.
  • the customization of the treatment for a particular disease according to the genetic profile of an individual is the basis of pharmacogenomics.
  • MYOC genetic profile The information gathered on the nature of the genetic defect (MYOC genetic profile), as determined from the transcriptional and translational profiles of MYOC, may be used alone, or in conjunction with information on other defects contributing or causing the same disease (disease genetic profile).
  • the goal of pharmacogenomics is to permit the selection of drugs or the design of drug treatment that are not only expected to be effective, but also, to be safe for a particular patient or patient population (i.e. a group of patients having the same genetic defect or profile).
  • the transcriptional and translational profiles may be used to monitor the effectiveness of a drug/therapeutic treatment. This will determine whether the treatment is effective or whether it should be altered and optimized.
  • the scope of the invention is extended to include the monitoring of drug effectiveness in clinical trials.
  • the method of determining the effectiveness of the drug candidate comprise the following steps:
  • the invention includes the novel drugs/therapeutics identified using the assays described above and their uses thereof for the prevention and treatment of the disease. 5.5 Other human genetic diseases and their genetically linked genes.
  • MYOC linkage gene
  • Glaucoma retina degenerative diseases and cardiovascular diseases, as the genetic diseases.
  • the scope of the current invention includes the application of the above specification to any gene or genes and the corresponding human genetic diseases whereby the said gene or genes has been found to be genetically linked to the said human genetic diseases.
  • the following set of linkage gene(s)/genetic diseases(s) are therefore also included within the scope of the invention.
  • BBS Bardet-Biedl syndrome
  • Hailey-Hailey disease ATP2C1 8. Alzheimer's disease Genes encoding for: Presenilin 1,
  • Presenilin 2 Presenilin 2, and Amyloid Precursor protein.
  • Fingerprinting techniques to diagnosis people with glaucoma are Fingerprinting techniques to diagnosis people with glaucoma.
  • a genetic profile i.e. 'fingerprint'
  • wild type i.e. full length
  • shorter either with a deletion or truncation
  • mRNAs messenger ribonucleic acids
  • MYOC Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or body fluids (for example Aqueous humor, Viteous humor, peripheral blood cells, urine etc.).
  • MYOC cDNAs by the polymerase chain reaction (PCR) using MYOC specific primers (pair, forward and reverse) whose DNA sequences are derived either from the coding [i.e. Open reading frame (ORF)] or from the non- coding regions (for example 5'-untranslated, promoter, 3 '-untranslated) of the MYOC gene, with any thermostable polymerase or related enzymes.
  • PCR polymerase chain reaction
  • the genetic profile derived from 1.7 may be compared to the genetic profile from a control (i.e. non-glaucoma individual).
  • the information provided by the genetic profile i.e. the position of the bands, the number of bands, the intensity of each individual bands
  • the information provided by the genetic profile may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have glaucoma. Prior calibration of this methodology with known glaucoma and non-glaucoma subjects is required.
  • the mRNAs are separated as described in 1.5 but under denaturating condition (for example in formaldehyde-gel based systems). 1.6 is modified to the
  • MYOC Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or body fluids (for example Aqueous humor, Viteous humor, peripheral blood cells, urine etc.).
  • the genetic profile derived from 2.6 may be compared to the genetic profile from a control (i.e. non-glaucoma individual).
  • the information provided by the genetic profile i.e. the position of the bands, the number of bands, the intensity of each individual bands
  • the information provided by the genetic profile may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have glaucoma. Prior calibration of this methodology with known glaucoma and non-glaucoma subjects is required.
  • a modification of the methodology in (2) uses the principle of immunoprecipitation.
  • the isolated proteins are mixed and incubated with the MYOC specific antibodies prior to their separation by gel-based electrophoresis. Proteins, which are not bound to the anti-MYOC antibodies are then removed (for example using protein A). Then steps 2.5, 2.6 and 2.7 as above.
  • Hybridization to high density oligonucleotide arrays to detect expression of MYOC This invention provides methods for the characterization of the expression levels and the pattern of expression of a multiplicity of MYOC nucleic acid forms. The methods involve obtaining a sample from a subject, hybridizing the nucleic acids (either mRNAs or the cDNAs derived from it) from the sample to a high density array of nucleic acids probes (either oligonucleotides or cDNA molecules, representing naturally occurring MYOC nucleic acid forms) where the high density array contains nucleic acid probes complementary to sequences and/or subsequences of target nucleic acids in the nucleic acid sample.
  • the method involves providing a pool of target nucleic acids (derived from a sample obtained from the subject) comprising RNA transcripts of one or more target forms, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of said nucleic acid probes immobilized on surface (for example glass, nylon etc.) where the array comprises more than 10, preferably more than 100, more preferably more than 1000, different nucleic acid probes and each different nucleic acid probe is localized in a predetermined region on the surface of the solid support microarray, the density of the different nucleic acid probes is greater than about 10, preferably greater than 50, more preferably greater than 100, per 1 cm 2 , and the nucleic acid probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the microarray.
  • the array comprises more than 10, preferably more than 100, more preferably more than 1000, different nucleic acid probes and each different nucle
  • the use of the oligonucleotides on the array is substituted with nucleic acids of actual characterized MYOC shorter forms, as follows:
  • the 'library' of cDNA clones are applied onto a solid support (for example glass, nylon memebrane) at high density in a grid-like array (this constitute the cDNA microarray), by spotting, or 'printing' or other techniques well known in the art, followed by the immobilization of the cDNAs on the support.
  • a solid support for example glass, nylon memebrane
  • the cDNA microarrays (identical copies of the microarray having being made in 3.2) are hybridized with single stranded cDNA probes that are derived from the mRNA isolated from the individual under investigation (as outlined in 1.1 to 1.3).
  • the probes are radioactively labelled, and the signal are visualized by autoradiography, but other detection methods may also be used (i.e. non-radioactive labels used).
  • Hybridization and the subsequent washing steps are performed to provide a high level of stringency so that incompletely hybridized probes will be unstable and will not give rise to a detectable signal.
  • the resulting pattern of hybridization may then be compared to the pattern profile from a control (i.e. non-glaucoma individual).
  • the information provided by the pattern profile (i.e. the location of the 'dots', the number of dots, the intensity of each individual dots) may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have glaucoma. Prior calibration of this methodology with known glaucoma and non- glaucoma subjects is required.
  • the present invention describes methodologies for the diagnosis/prognosis of retinal diseases in human subjects, whether the individual is asymptomatic or have clinical symptoms.
  • the invention makes use of the recent finding (T. H. Kong, unpublished results) that both wild type (i.e. full length) and shorter (either with deletion or truncation) forms of the Trabecular meshwork Inducible Glucocorticoid Response protein (MYOC, also called Myocilin (MYO)) and their messenger ribonucleic acids (mRNAs) are present in ocular and non-ocular tissues. More importantly, these shorter forms are differentially expressed between normal and diseased individuals.
  • MYOC Trabecular meshwork Inducible Glucocorticoid Response protein
  • mRNAs messenger ribonucleic acids
  • Age Related Macular Degeneration Retinitis Pigmentosa, Usher Syndrome, Stargardt Disease, Bardet-Biedl Syndrome, Best Disease, Choroideremia, Juvenile Retinoschisis, Leber Congenital Amaurosis, Blue-Cone Monochromacy, Central Areolar Choroidal Dystrophy, Cone-Rod Dystrophy, Cone Dystrophy, Congenital Stationary Night Blindness, Dominant Drusen, Goldmann-Favre Dystrophy, Gyrate Atrophy, Kearns-Sayre Syndrome, Macular Drusen, Macular Dystrophy, Malattia Leventinese, Oguchi Disease, Refsum Disease, Atypical RP, Retinitis Punctata Albescens, Rod Dystrophy, Rod-Cone Dystrophy, Rod Monchromatism, Sector RP, Sorsby Fundus Dystrophy, Sjo
  • a genetic profile i.e. 'fingerprint'
  • wild type i.e. full length
  • shorter either with a deletion or truncation
  • mRNAs messenger ribonucleic acids
  • MYOC Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or body fluids (e.g. Aqueous humor, Viteous humor, blood sample, urine etc.).
  • body fluids e.g. Aqueous humor, Viteous humor, blood sample, urine etc.
  • MYOC cDNAs by the polymerase chain reaction (PCR) using MYOC specific primers (pair, forward and reverse) whose DNA sequences are derived either from the coding [i.e. Open reading frame (ORF)] or from the non- coding regions (e.g. 5 '-untranslated, promoter, 3 '-untranslated) of the MYOC gene, with any thermostable polymerase or related enzymes.
  • PCR polymerase chain reaction
  • the genetic profile derived from 1.7 may be compared to the genetic profile from a control (i.e. normal individual).
  • the information provided by the genetic profile i.e. the position of the bands, the number of bands, the intensity of each individual bands
  • the information provided by the genetic profile may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have a retinal disease. Prior calibration of this methodology with individuals known to have the disease and non-diseased subjects is required.
  • the mRNAs are separated as described in 1.5 but under denaturating condition (e.g. in formaldehyde-gel based systems).
  • 1.6 is modified to the Northern transfer protocol, with 1.7 and 1.8 as described above.
  • MYOC Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or body fluids (e.g. Aqueous humor, Viteous humor, blood sample, urine etc.).
  • the genetic profile derived from 2.6 may be compared to the genetic profile from a control (i.e. normal individual).
  • the information provided by the genetic profile i.e. the position of the bands, the number of bands, the intensity of each individual bands
  • the information provided by the genetic profile may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have a retinal disease. Prior calibration of this methodology with individuals known to have the disease and non-diseased subjects is required.
  • a modification of the methodology in (2) uses the principle of immunoprecipitation.
  • the isolated proteins are mixed and incubated with the MYOC specific antibodies prior to their separation by gel-based electrophoresis. Proteins, which are not bound to the anti-MYOC antibodies are then removed (e.g. using protein A). Then steps 2.5, 2.6 and 2.7 as above.
  • Hybridization to high density oligonucleotide arrays to detect expression of MYOC This invention provide methods for the characterization of the expression levels and the pattern of expression of a multiplicity of MYOC nucleic acid forms.
  • the methods involve obtaining a sample from a subject, hybridizing the nucleic acids (either mRNAs or the cDNAs derived from it) from the sample to a high density array of nucleic acids probes (either oligonucleotides or cDNA molecules, representing naturally occurring MYOC nucleic acid forms) where the high density array contains nucleic acid probes complementary to sequences and/or subsequences of target nucleic acids in the nucleic acid sample.
  • the method involves providing a pool of target nucleic acids (derived from a sample obtained from the subject) comprising RNA transcripts of one or more target forms, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of said nucleic acid probes immobilized on surface (e.g.
  • the array comprises more than 10, preferably more than 100, more preferably more than 1000, different nucleic acid probes and each different nucleic acid probe is localized in a predetermined region on the surface of the solid support microarray, the density of the different nucleic acid probes is greater than about 10, preferably greater than 50, more preferably greater than 100, per 1 cm 2 , and the nucleic acid probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the microarray.
  • the use of the oligonucleotides on the array is substituted with nucleic acids of actual characterized MYOC shorter forms, as follows:
  • the 'library' of cDNA clones are applied onto a solid support (e.g. glass, nylon memebrane) at high density in a grid-like array (this constitute the cDNA microarray), by spotting, or 'printing' or other techniques well known in the art, followed by the immobilization of the cDNAs on the support.
  • a solid support e.g. glass, nylon memebrane
  • the cDNA microarrays (identical copies of the microarray having being made in 3.2) are hybridized with single stranded cDNA probes that are derived from the mRNA isolated from the individual under investigation (as outlined in 1.1 to 1.3).
  • the probes are radioactively labelled, and the signal are visualized by autoradiography, but other detection methods may also be used (i.e. non-radioactive labels used).
  • Hybridization and the subsequent washing steps are performed to provide a high level of stringency so that incompletely hybridized probes will be unstable and will not give rise to a detectable signal.
  • the resulting pattern of hybridization may then be compared to the pattern profile from a control (i.e. normal individual).
  • the information provided by the pattern profile (i.e. the location of the 'dots', the number of dots, the intensity of each individual dots) may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have a retinal disease. Prior calibration of this methodology with individuals known to have the disease and normal subjects is required.

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Abstract

Genetic profiling methodologies for the prognosis and/or diagnosis of Glaucoma, Retinal degenerative diseases or cardiovascular diseases, and thei uses thereof in screening assays for the identification of therapeutics and the evaluation of their effectiveness for treating Glaucoma, Retinal degenerative diseases or cardiovascular diseases in a subject are described.

Description

Diagnostics and therapeutics for Glaucoma, Retinal Degenerative diseases and Cardiovascular diseases based on novel nucleic acid and protein forms of myocilin (MYOC).
Inventor: Tim H. Kong, White Plains, New York.
Related U.S. Application Data
Provisional application No. 60/281,422, April 5, 2001 Provisional application No. 60/306,889 July 23, 2001
References Cited
Alward WLM, Fingert JH, Coote MA. Clinical features associated with mutations in the chromosome 1 open-angle glaucoma gene (GLCIA). N Engl J Med. 1998; 338:1022- 1027.
Fodor et al., "Light-Directed, Spatially addressable Parallel Chemical Synthesis." Science, 251 :767-773 (1991).
Khrapko et al., "A Method for DNA-Sequencing by Hybridization with Oligonucleotide Matrix." DNA Sequencing and Mapping, 1:375-388 (1991).
Lehrach et al., "Hybridization Fingerprinting in Genome Mapping and Sequencing." in Genome Analysis, vol.l: Genetic and Physical Mapping. (K.E. Davies & S.M. Tilgham, Eds.) Cold Spring Harbor Laboratory Press, pp.39-81 (1990). Mao K, Stewart WC, Shields MB Correlation between intraocular pressure control and progressive glaucomatous damage in primary open-angle glaucoma. Am J Ophthalmol. 1991; 111:51-55.
Nguyen TD, Chen P, Huang WD, Chen H, Johnson D, Polansky JR. Gene structure and properties of MYOC, an olfactomedin-related glycoprotein cloned from glucocorticoid- induced trabecular meshwork cells. J Biol Chem. 1998; 273:6341-6350.
Pirrung, et al., "Comparison of Methods fro Photochemical Phosphoramidite-Based DNA Synthesis." J. Org. Chem., 60:6270-6276 (1995).
Polansky JR. HTM cell culture model for steroid effects on IOP: overview. LutjenDrecoll
E, ed. Basic Aspects of Glaucoma Research III. Stuttgart, Germany: Schattauer;
1993:307-318.
Quigley HA and Maumenee E. Long-term follow-up of treated open- angle glaucoma. Am
J Ophthalmol. 1979; 87:519-525.
Sambrook, et al., "Molecular Cloning, A Laboratory Manual." Cold Sprig Habor Press, pp. 7.39-7.52 (1989).
Snyder AD, Rivers AM, Yokoe H, Menco BPM, Anholt RH. Olfactomedin: purification, characterization, and localization of a novel olfactory glycoprotein. Biochemistry. 1991; 30:9143-9153.
Southern, et al., "Analyzing and Comparing Nucleic Acid Sequences by Hybridization to Arrays of Oligonucleotides; Evaluation Using Experimental Models." Genomics, 13:1008-1017 (1992).
Stone EM, Fingert JH, Alward WLM, et al. Identification of a gene that causes primary open-angle glaucoma. Science. 1997; 275:668-670. Yokoe H and Anholt RR Molecular cloning of olfactomedin, an extracellular matrix protein specific to olfactory neuroepithelium. Proc Natl Acad Sci U.S.A. 1993; 90:4655- 4659.
Abstract
Genetic profiling methodologies for the prognosis and/or diagnosis of Glaucoma, Retinal degenerative diseases or cardiovascular diseases, and their uses thereof in screening assays for the identification of therapeutics and the evaluation of their effectiveness for treating Glaucoma, Retinal degenerative diseases or cardiovascular diseases in a subject are described.
36 Claims
Diagnostics and therapeutics for Glaucoma, Retinal Degenerative deseases and Cardiovascular diseases based on novel nucleic acid and protein forms of MYOC (MYOC).
This application claims priority to the following provisional patent applications: Provisional application No. 60/281,422, filed April 5, 2001 Provisional application No. 60/306,889, filed July 23, 2001
GOVERNMENT FUNDING
This invention was partially funded by the NIH NEI Grants EY04873 and EY08672; the government, therefore, has certain rights to the invention.
1. FIELD OF THE INVENTION
The invention primarily relates to the "fingerprinting of nucleic acids or proteins', that is, the generation of a signature characteristic of the base sequence of a nucleic acid template, or the base sequence of a protein, respectively.
2. BACKGROUND OF THE INVENTION
2a. Glaucoma
Glaucoma is a group of eye diseases, that here in the United States, is the second leading cause of legal blindness, and the leading cause of blindness in African- American individuals. The most common form of the glaucoma, is Primary open angle glaucoma (POAG), which affects about 2% of the population over age 40. Nearly 12,000 people each year are blinded by this disorder in this country alone. The Juvenile form of this disorder, Juvenile open angle glaucoma (JOAG), affects individuals at an earlier age. The gene linked to this form of glaucoma has recently been cloned and identified to be the MYOC gene (Stone et al., 1997), but published research data shows that only about 4% of glaucoma patients have genetic mutations in the gene. The present invention is based, on the recent finding by the inventor (T. H. Kong, unpublished results) that in addition to the wild type (i.e. full length), shorter messenger ribonucleic acids transcripts (e.g. mRNAs with a deletion) of the gene for the Trabecular meshwork Inducible Glucocorticoid Responsive protein (TIGR), also known as the Myocilin protein (MYOC), are expressed in cells of ocular and non-ocular origin of the human body. In addition, from studies on ocular tissues, these shorter mRNAs have shown to be differentially expressed in normal and Glaucoma subjects. Methodologies described by the current invention can be used for the prognosis and/or diagnosis of people with glaucoma whether they are asymptomatic or have clinical symptoms, at any stage of the disease.
Genetic probes and methods of use thereof in the prognosis/diagnosis of glaucoma are described herein. The invention relates particularly to probes and methods for evaluating MYOC mRNA species that are differentially expressed in diseased compared to normal individuals.
2b. Retinal Degenerative diseases
Retinal degenerative diseases (RDD) are disorders that lead to the degeneration of the retina. Degeneration of the retina impairs the ability to see, leading to legal, if not complete blindness. Over 6 million Americans are losing sight to one of these diseases.
Every American is at risk, regardless of age or race. The three most common forms of retinal degenerative diseases are Retinitis Pigmentosa (RP), Macular degeneration (MD), and Usher Syndrome.
The present invention is based, on the recent finding by the inventor (T. H. Kong, unpublished results) that in addition to the wild type (i.e. full length), shorter messenger ribonucleic acids transcripts (e.g. mRNAs with a deletion) of the gene for the Trabecular meshwork Inducible Glucocorticoid Responsive protein (TIGR), also known as the Myocilin protein (MYOC), are expressed in cells of ocular and non-ocular origin of the human body. In addition, from studies on ocular tissues, these shorter mRNAs have shown to be differentially expressed in normal and retinal diseased individuals. Methodologies described by the current invention can be used for the prognosis/diagnosis of people with RDD whether they are asymptomatic or have clinical symptoms, at any stage of the disease.
Genetic probes and methods of use thereof in the prognosis/diagnosis of RDD are described herein. The invention relates particularly to probes and methods for evaluating the presence of MYOC mRNA species that are differentially expressed in retina diseased subjects compared to normal subjects.
2c. Cardiovascular diseases
In the United States, cardiovascular diseases ranks as the leading cause of death. Worldwide, the diseases cause 12 million deaths each year (third monitoring report of the World Health Organization, 1991-93).
Cardiovascular diseases result from pathological processes affecting either, the heart- muscle (myocardium), its lining membrane (endocardium), or its outer covering and enclosing sac (pericardium). Of the many types of diseases, Arteriosclerotic heart diseases are the most common and account for most of the cardiac deaths in the world. The gene for the Trabecular meshwork Inducible Glucocorticoid Responsive protein (TIGR), also known as Myocilin (MYOC), is expressed in the heart. The present invention is based, on the recent finding by the inventor (T. H. Kong, unpublished results) that in addition to the wild type (i.e. full length), shorter messenger ribonucleic acids transcripts (e.g. mRNAs with a deletion) of the gene for the Trabecular meshwork Inducible Glucocorticoid Responsive protein (TIGR), also known as the Myocilin protein (MYOC), are expressed in cells of ocular and non-ocular origin of the human body. In those ocular and non-ocular tissues that have been examined, where the wild type MYOC transcript is known to be expressed, the shorter MYOC mRNA species have been detected also. In addition, the inventor has demonstrated that the wild type and novel (i.e. shorter) forms of the MYOC mRNA are differentially expressed in normal and diseased individuals in other tissues, in relation to other genetic disorders.
Methodologies described by the current invention can be used for the prognosis/diagnosis of people with cardiovascular diseases whether they are asymptomatic or have clinical symptoms, at any stage of the disease. Genetic probes and methods of use thereof in the prognosis/diagnosis of cardiovascular disease are described herein. The invention relates particularly to probes and methods for evaluating the presence of MYOC mRNA species that are differentially expressed in diseased individuals compared to normal individuals.
2d. Fingerprinting technologies
Improved diagnostics for the genetically-based diseases of Glaucoma, Retinal Degenerative diseases and cardiovascular diseases are needed, particularly to enable detection of these diseases far earlier than is currently possible with available technologies in the prior art. This has obvious benefits for the prevention and treatment of these genetic diseases. The invention includes a variety of methodologies for generating genetic profiles or 'fingerprints' for prognostic and diagnostic use. Within the scope of the invention are methodologies for the making of microarrays of biological macromolecules (for example, microarrays of nucleic acid molecules or proteins), the generation of biopolymers for fabricating on microarrays, and their uses thereof. In addition, the use of microarrays to generate genetic 'fingerprints' do not rely on the rate- limiting step of gel electrophoresis, and can therefore, produce a large number of genetic profiles in a short time.
3. Definitions For convenience, the meaning of certain terms and phrases employed in the specification and appended claims, unless stated otherwise, are as provided below:
The term "disease(s)" refers to a Glaucoma disease, or to a Retinal Degenerative disease, or to a cardiovascular disease. The terms "Glaucoma" or "Glaucoma disease" refers to a collection of different eye diseases that are characterized by a specific pattern of damage to the optic nerve, and a loss in the visual field. The terms includes the various types of glaucoma, including Primary open angle glaucoma, juvenile open angle glaucoma, normal tension glaucoma, angle closure glaucoma, acute glaucoma, pigmentary glaucoma, etc. Most types, but not all, are associated with an elevation in the intraocular pressure. This is not the disease itself, but a major risk factor in the development of glaucoma.
The term "Retinal degenerative diseases" (RDD) refers to all Retinal degenerative diseases and the following is not intended to be an exhaustive list: Age Related Macular Degeneration, Retinitis Pigmentosa, Usher Syndrome, Stargardt Disease, Bardet-Biedl Syndrome, Best Disease, Choroideremia, Juvenile Retinoschisis, Leber Congenital Amaurosis, Blue-Cone Monochromacy, Central Areolar Choroidal Dystrophy, Cone-Rod Dystrophy, Cone Dystrophy, Congenital Stationary Night Blindness, Dominant Drusen, Goldmann-Favre Dystrophy, Gyrate Atrophy, Kearns- Sayre Syndrome, Macular Drusen, Macular Dystrophy, Malattia Leventinese, Oguchi Disease, Refsum Disease, Atypical RP, Retinitis Punctata Albescens, Rod Dystrophy, Rod-Cone Dystrophy, Rod Monchromatism, Sector RP, Sorsby Fundus Dystrophy, Sjogren-Larsson Syndrome.
The term "cardiovascular diseases" refers to all cardiovascular diseases and the following is not intended to be an exhaustive list:
Congenital heart diseases (for example, Patent ductus arteriosus, Pulmonary stenosis,
Aortic stenosis, Coarctation of the aorta, Bicuspid aortic valve, Subaortic stenosis,
Ebstein's anlmaly, Atrial septal defect, Ventricular septal defect, Atrioventricular canal defect, Tetralogy of Fallot, Transposition of the great arteries, Tricuspid atresia,
Pulmonary atresia, Truncus arteriosus, Total anomalous pulmonary venous connection,
Hypoplastic left heart syndrome, etc.).
Diseases affecting the myocardium (for example, Acute myocardium, chronic myocardium, Myocardial ischaemia, etc.). Stroke (for example, cerebral thrombosis, cerebral embolism etc.). Diseases affecting the endocardium (for example, Acute endocarditis, rheumatic heart disease, etc.).
Hypertensive heart diseases (any cardiac diseases having an elevated blood pressure component).
Arteriosclerotic heart diseases (any coronary diseases involving the thickening or hardening of the arteries). Diseases affecting the pericardium (for example, Pericarditis, etc.)
Disorders of cardiac rhythm (for example, Arrhythmias, tachycardia, bradycardia, ventricular tachycardia, ventricular fibrillation, atrial fibrillation etc.).
Heart-block (any disease or degeneration of the 'pacemaker' causing partial or complete arrest of the impulses governing the heart beat).
The term 'nucleic acids", as used herein, refers to oligonucleotides (for example, when referring to primers or probes) or polynucleotides (for example, when referring to probes, DNA fragments, genes) of deoxyribonucleic acid (DNA) or, where appropriate, ribonucleic acid (RNA). It is also understood to include nucleotide analogs of DNA or RNA, and the nucleic acids may be single (sense or antisense) or double-stranded.
The term "MYOC nucleic acid", as used herein, refers to a nucleic acid encoding an MYOC polypeptide, such as nucleic acids having SEQ ID NOS. 1 or 3, as well as fragments thereof, complements thereof, and derivatives thereof, and is intended to include the novel deleted and truncated forms, of figure 4 and any other naturally occurring shorter forms.
The terms "protein", "polypeptide" and "peptide" are used interchangeably herein when referring to a gene product. In addition, the terms "MYOC polypeptide" and "MYOC protein", as used herein, are intended to include polypeptides having the amino acid sequence shown as SEQ ID NO. 2 or fragments thereof, and is intended to include the novel deleted and truncated forms (i.e. the translation products, of figure 4 and any other naturally occurring shorter forms), and homologs thereof and include agonist and antagonist polypeptides. The terms "allele", and "allelic variant", used interchangeably herein, refers to different forms of a gene or portions thereof. Different alleles or allelic variants of a gene can differ from each other by a single nucleotide, or more. They include differences arising from a deletion, an insertion, a substitution, a rearrangement, (i.e. differences arising from a mutational event). Alleles of the same gene occupy the same position or locus on homologous chromosomes. A subject having two identical alleles of a gene, is said to be homozygous for the gene or allele. On the other hand, if the subject has two different alleles for the gene, the subject is said to be heterozygous for that gene. Therefore, the term "allelic variant of a polymorphic region of a MYOC gene" or words to that effect, refers to a region of a MYOC gene having one or several nucleotide sequences found in that region of the gene in other individuals. Also, the term "wild type allele", or words to that effect, refers to an allele or form of a gene which when present in both copies will result in a subject having the wild type phenotype. As some nucleotide sequence changes may not result in amino acid changes, and furthermore, as some amino acid changes may not result in a change of the phenotype, there can be several different or alternative forms of the wild type allele for a specific gene.
As used herein, the term "Antagonist" refers to an agent or compound which can downregulate (for example, suppresses or inhibits) one or more of MYOC bioactivities. This could occur by downregulating the expression of a MYOC gene or by reducing the amount of MYOC protein present. It could also occur by inhibiting or decreasing the interaction between a MYOC protein and another molecule, for example, an upstream region of a gene, which is regulated by a MYOC transcription factor. The MYOC antagonist can be a MYOC antisense nucleic acid, or a nucleic acid encoding a dominant negative form of a MYOC polypeptide, or it can be a ribozyme which can interact specifically with a MYOC RNA. Further MYOC antagonists can be peptides, antibodies and small molecules, which is capable of binding to a MYOC polypeptide and inhibiting its action.
As used herein, the term "Agonist" refers to an agent or compound which can upregulate (for example, supplements or potentiates) one or more of MYOC bioactivities. This could occur by upregulating the expression of a MYOC gene or by increasing the amount of MYOC protein present. It could occur by enhancing or increasing the interaction between a MYOC protein and another molecule, for example, an upstream region of a gene, which is regulated by a MYOC transcription factor. The MYOC agonist can be peptides, antibodies and small molecules, which is capable of binding to a MYOC polypeptide and enhancing its action.
The term "activity", as used herein, has the same meaning as " Bioactivity", or "Biological activity" or "biological function", and refers to the effector or antigenic function performed directly or indirectly by a MYOC polypeptide (either native or denatured form), or by any parts thereof. The biological activities include binding to a target nucleic acid (for example, an upstream region of a gene, which is regulated by a MYOC transcription factor), and a MYOC bioactivity can be altered by directly affecting an MYOC polypeptide, or by changing the level of a MYOC polypeptide (e.g. by modulating the expression of a MYOC gene).
The term "Identity", as used herein, has the same meaning as "Similarity", or "Homology", and refers to the degree of similarity between two or more polypeptide sequences, or between two or more nucleic acid sequences. The sequences may be aligned and compared with respect to a particular position in the sequence. If the same amino acid or base is found at the position, then the sequences are said to be identical at that position. The sum of all the identical matches throughout the aligning sequences is then a measure of the degree of similarity between them. A sequence "unrelated" to the subject myocilin sequences of the invention will share less than 38% sequence identity with them, preferably less than 24% sequence identity.
As used herein, the terms "cells", or "host cells", shall have the same meaning and is understood to refer not only to the particular subject cells, but also within the scope of the terms, to the progeny or potential progeny of the subject cells. It is also understood that the cells may undergo mutational events or subjected to environmental influences and therefore the progeny cells may not be identical to the subject cells from which they are derived.
The terms "complementary " and "complement" are used interchangeable herein. The complement of a nucleic acid strand can refer to the complement of a coding strand or the complement of a non-coding strand. Therefore, the term "nucleotide sequence complementary to the nucleic acid set forth in SEQ ID No. x" refers to the nucleic acid that is the complementary strand to the nucleic acid strand set forth in SEQ ID No. x. The nucleotide sequences and the complementary nucleotide sequences are always given in the 5' to 3' direction.
A gene may have one or more copies in the genome. Where there are multiple copies, each copy may differ in the nucleotide sequence, due to deletions, insertions, rearrangements etc., but which may encode essentially the same polypeptide with substantially the same activity. Therefore, the term " DNA sequence encoding a MYOC polypeptide", or words to that effect, is meant to refer to all the MYOC genes in an individual. Differences in sequences due to allelic differences between individuals are also understood to be within the scope of the term.
As used herein, the term "MYOC therapeutics", refers to various MYOC polypeptide forms, nucleic acids, peptidomimetics, or any small molecules, which are able to alter or modulate one or more activities of a wild type MYOC protein or that of the MYOC protein binding partner (MPBP). A MYOC therapeutic, which is able to mimic, potentiate, or upregulate one or more activities of a wild type MYOC protein or the MPBP is a "MYOC agonist". Likewise, a MYOC therapeutic, which is able to inhibit, suppress, or downregulate one or more activities of a wild type MYOC protein or the MPBP is a "MYOC antagonist".
As used herein, the term "interact" refers to any detectable associations between molecules, preferably biochemical associatons. It is understood to include interactions of protein-protein, protein-nucleic acid, nucleic acid-nucleic acid, protein-small molecules, nucleic acid-small molecules. The term "sample" as used in the context "...a sample obtained from a subject..." as used herein, is meant to refer to tissues, cells, or bodily fluids (for example Aqueous humor, Vitreous humor, tears, blood, saliva, urine etc.) either of an ocular or non-ocular origin.
As used herein, the term "isolated" as applied to nucleic acids (i.e. DNA and RNA), refers to nucleic acids encoding a MYOC polypeptide that is separated from other DNAs and RNAs that are naturally or orginally present in the source. An isolated MYOC nucleic acid usually has less than 8 kilobases of flanking sequences, and preferably less than 2 kilobases of flanking sequences, on either side of the gene. As applied to polypeptides, the term refers to MYOC polypeptides, either recombinant or purified, that are separated from other cellular proteins, nucleic acids, and small molecules. When applied to nucleic acids or polypeptides produced by recombinant means, it is understood that the nucleic acid or polypeptide is substantially free of cellular, viral or culture materials.
As used herein, the term "mutation" refers to alterations to the nucleotide sequence of a gene, or the amino acid sequence of the gene product. The term includes deletions, insertions, rearrangements, or single base or amino acid substitutions. MYOC mutations that are likely to contribute or cause the disease can occur at the DNA level (genomic mutations) or at the transcript level. At the mRNA level, the term includes the shorter MYOC forms, documented in figure 4 and any other naturally occurring shorter forms. The terms "mutated gene", or "mutated allele", as used herein, refers to the allelic forms of the gene (i.e. not wild type) that are capable of altering the phenotype of the individual (for example, normal state to disease state).
The term "non-human animals", as used herein, is intended to refer to the following list, not intended to be exhaustive; chickens, cow, dog, sheep, non-human primates, amphibians, reptiles, etc., preferably to rodents (e.g. rats) and more preferably, to mice. "Transgenic or chimeric animals", on the other hand, refers to animals, which harbors the recombinant gene, or the transgene, or the heterologous gene, or animals expressing such a gene, or animals where such a gene is expressed in some cells but not in others.
The term "polymorphism", as used herein, refers to the coexistence of two or more forms (i.e. two or more different sequences) of a gene (e.g. allelic variant) or part thereof, within an individual or between individuals. The polymorphism may arise due to a single nucleotide difference (as in SNP polymorphism) or can be several nucleotides or more long A "polymorphic gene" is a gene which has one or more polymorphic region (i.e. a region exhibiting polymorphism)..
The term "promoter", as used herein, refers to a DNA sequence that regulates expression of a specific DNA sequence that is operatively linked to it. The term includes "constitutive promoters" (i.e. requires no induction for expression), and "inducible promoters" (i.e. expression can be controlled). The term also includes "leaky promoters" (i.e. expression takes place primarily, but not exclusively, in certain cells, or under certain conditions) and "tissue-specific promoters" (i.e. can regulate expression in specific cells of a tissue or tissues, and no others).
As used herein, the term "small molecule" refers to nucleic acids, peptides, polypeptides, peptidomimetics, lipids, carbohydrates, organic (i.e. carbon containing) or inorganic entities, having a molecular weight of less than 6 kilodaltons (kD), preferably less than 5 kD, and more preferably less than 4 kD. Many companies (e.g. pharmaceutical companies), have extensive libraries of small molecules of various origins (e.g. chemical, bacterial, fungal, etc) which can be used in the screening assays of the invention to identify compounds that are able to modulate one or more activities of myocilin.
The term "support", as used herein and in the context of hybridization or interacting molecules, shall include but not limited to, a porous or non-porous membrane, a polyacrylamide layer, a substrate, a glass or microscope slide, etc..
The term "specifically hybridizes", as used herein, is meant to refer to the ability of a nucleic acid molecule of the current invention to hybridize or bind to a target molecule of at least approximately 7, 14, 21, 28, 50, 100, 150, 200, 300, 350, 400, 450 or 500 consecutive nucleotides. Preferably, the target molecule is a vertebrate gene, more preferably a MYOC gene.
The term "distinct biopolymers", as applied to the biopolymers forming an array or microarray, means a member which is distinct from other members on the basis of (1) a different biopolymer sequence, and/or (2) a different amount or concentration of the same or distinct biopolymers, or (3) a different mixture of two or more distinct biopolymers. Thus, an array/microarray of "distinct polynucleotides" means an array/microarray containing, as its members, (1) polynucleotides of different sequences, and/or (2) polynucleotides differing in amount or concentration, or (3) polynucleotides of different mixtures of two or more distinct members.
The term "Cell type", as used herein and in the context of an array/microarray, means a cell from a given source. This given source can be, for instance, a tissue, or organ, or a cell with a given pathology or genetic makeup, or a cell in a given state of differentiation.
An "array" is a linear or two-dimensional array of preferably discrete regions, each possessing a finite area and formed on a solid support surface. A "microarray" is an array of preferably discrete regions, possessing a density of discrete regions of 10/cm2 or greater, and preferably at 50/cm or greater, more preferably 250/cm or greater. The regions in a microarray have typical dimensions, for instance diameters in the range of about 8 to 300 μm, and are separated from each other in the array by about the same.
The term "Ligand" refers to one member in a ligand/anti-ligand pair, and include for instance, an effector molecule in an receptor/effector binding pair; one of the nucleic acid strands in a complementary, hybridized nucleic acid duplex binding pair; or an antibody/antigen or antibody fragment/antigen binding pair. "Anti-ligand" refers to the opposite member in the above-mentioned pairs of molecules. An "analyte" refers to a macromolecule, for instance a polynucleotide or polypeptide, or antibody whose presence, identity, and/or amount is to be determined. The analyte is a member of a ligand/anti-ligand pair. Preferably, the analyte are the molecules of the current invention.
The term "transcriptional profile", as used herein, refers to the expression or the presence of all transcripts of MYOC (i.e. pattern of expression) and their levels of expression. Thus, this is both a qualitative and quantitative profile of MYOC expression at the transcript level. The term "translational profile", as used herein, refers to the expression or the presence of all polypeptides of MYOC (i.e. pattern of expression) and their levels of expression. Thus, this is both a qualitative and quantitative profile of MYOC expression at the protein level.
4. BRIEF DESCRIPTION OF FIGURES 1-4
Figure 1 is the cDNA sequence of the human MYOC gene, including the 5' and 3' untranslated region (UTRs) (SEQ ID No.l).
Figure 2 is the 1512 base pair Open reading frame (ORF) of the human MYOC gene, provided herein as SEQ ID No.3.
Figure 3 is the 504 amino acid sequence of the human MYOC protein, provided herein as
SEQ ID No.2.
Figures 4a, 4b and 4c are figures depicting and listing some of the deleted MYOC cDNAs that has been identified and characterized.
5. DETAILS OF THE INVENTION 5.1 Fingerprinting techniques to generate transcriptional and translational profiles. Three main methodologies are disclosed for the generation of a genetic profile (i.e. 'fingerprint') based on the expression of both the wild type (i.e. full length) and shorter (either with a deletion or truncation) forms of the myocilin (MYOC) mRNA species and the gene product (i.e. polypeptides) that they encode.
[Myocilin is also known as the Trabecular meshwork Inducible Glucocorticoid Responsive protein (TIGR)].
1. The detection of the full-length and shorter forms of the MYOC mRNAs or the complementary Deoxyribonucleic acids (cDNAs) that are derived from it.
2. The detection of the full-length and shorter forms of the MYOC protein
3. The use of microarrays or biochips to detect 1 and 2 above.
1. The detection of the full-length and shorter forms of the MYOC cDNA/mRNA 77je detection of the full-length and shorter forms of the MYOC cDNA
1.1 Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or bodily fluids (for example Aqueous humor, Viteous humor, tears, blood, urine etc.).
1.2 Isolate mRNAs from 1.1
1.3 Synthesize cDNAs (either single stranded cDNA or double stranded cDNA) from 1.2
1.4 Amplification of MYOC cDNAs by the polymerase chain reaction (PCR) using MYOC specific primers (pair, forward and reverse) whose DNA sequences are derived either from the coding [i.e. Open reading frame (ORF)] or from the non- coding regions (for example, 5'-untranslated, promoter, 3'-untranslated) of the MYOC gene, with any thermostable DNA polymerase or related enzymes (e.g. Taq).
1.5 Separation of the PCR products from 1.4 (for example, by electrophoresis on gel- based medium such as agarose gels).
1.6 Transfer of the separated DNA fragments by Southern transfer onto a solid support (for example, nitrocellulose, nylon membranes). Alternatively, the separation medium of 1.5 (e.g. agarose gel) may be dried and used directly for hybridization.
1.7 Hybridization of the PCR products immobilized on the solid support (or separation medium such as the gel after being dried) with a radioactively labeled DNA or RNA probe derived from MYOC, and subsequent visualization of the hybridization signals by autoradiography. Other methods of detection may also be used (i.e. non- radioactive labels, such as fluorescent labels or enzymatic labels). 1.8 The genetic profile (i.e. the transcriptional profile) derived from 1.7 (i.e. the "barcodes' or the 'fingerprint') may be compared to the genetic profile from a control (i.e. non-diseased individual). The information provided by the genetic profile [i.e. the position of the bands, the number of bands, the intensity (or color, where a colorimetric or fluorescent label is used) of each individual bands] may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have the disease. Prior calibration of this methodology with known disease and non-diseased subjects is required.
The detection of the full-length and shorter forms of the MYOC mRNA
An variation of the methodology in (1) allow for the detection of full-length and shorter forms of the MYOC mRNA:
After 1.1 and 1.2, the mRNAs are separated as described in 1.5 but under denaturating condition (for example, in formaldehyde-gel based systems). 1.6 is modified to the
Northern transfer protocol, with 1.7 and 1.8 as described above.
2. The detection of the full-length and shorter forms of the MYOC protein.
2.1 Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or bodily fluids (for example Aqueous humor, Viteous humor, tears, blood, urine etc.).
2.2 Lyse cells and/or isolate total cellular proteins
2.3 Separation of proteins (for example, by gel electrophoresis under denaturing or non- denaturing conditions such as SDS-PAGE, 2-D gel etc).
2.4 Transfer separated proteins from the gel medium to a solid support (for example, nylon membrane) using the Western blotting technique. Alternatively, the separation medium of 2.3 (e.g. polyacrylamide gel) may be dried and used directly for hybridization. 2.5 Detection of the immobilized proteins from 2.4 with single or multiple specific anti- MYOC antibodies (polyclonal or monclonal).
2.6 Visualization of the signals from 2.5 by autoradiography, as the antibodies used in 2.5 are conjugated or linked to a radioactive label. Other methods of detection may also be used (i.e. non-radioactive labels, such as fluorescent labels or enzymatic labels). To enhance the sensitivity of this method, primary and secondary antibodies may be used in a sandwich-type detection assay.
2.7 The genetic profile (i.e. the translational profile) derived from 2.6 (i.e. the "barcodes' or the 'fingerprint') may be compared to the genetic profile from a control (i.e. non- diseased individual).
The information provided by the genetic profile [i.e. the position of the bands, the number of bands, the intensity (or color, where a colorimetric or fluorescent label is used) of each individual bands] may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have the disease. Prior calibration of this methodology with known diseased and non-diseased subjects is required.
An variation of the methodology in (2) uses the principle of immunoprecipitation (IP). Here, after 2.1 and 2.2, the isolated proteins are mixed and incubated with the MYOC specific antibodies. Proteins, which are not bound to the anti-MYOC antibodies are then removed (for example, using protein A). This is followed by separation (for example, by gel-based electrophoresis) of the MYOC proteins. Then steps 2.5, 2.6 and 2.7 as above.
3. Hybridization to high density oligonucleotide arrays to detect expression of MYOC This invention provides methods for the characterization of the pattern of expression of a multiplicity of MYOC nucleic acid forms, and their expression levels. The methods involve obtaining a sample from a subject, hybridizing the nucleic acids (either mRNAs or the cDNAs derived from it) from the sample to a high density array of oligonucleotide probes (representing naturally occurring MYOC nucleic acid forms) where the high density array contains nucleic acid probes complementary to sequences or subsequences of target nucleic acids in the said nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids (derived from a sample obtained from the subject) comprising one or more target mRNA transcripts, or nucleic acids derived from the mRNA transcripts, hybridizing said pool of nucleic acids to an array of said nucleic acid probes immobilized on surface (for example, glass, nylon etc.) where the array comprises more than 50, preferably more than 500, more preferably more than 5000, different nucleic acid probes and each different nucleic acid probe is localized in a predetermined region on the surface of the solid support microarray, the density of the different nucleic acid probes is greater than about 10, preferably greater than 50, more preferably greater than 250 per 1 cm2, and the nucleic acid probes are complementary to the RNA transcripts (or nucleic acids derived from the RNA transcripts); qualifying and quantifying the hybridized nucleic acids in the microarray. The said pool of target nucleic acids is radioactively labeled. Other methods of detection may also be used (i.e. non-radioactive labels, such as fluorescent labels or enzymatic labels).
In an variation of the above method, the use of the oligonucleotides on the array is substituted with nucleic acids (e.g. DNA fragments) of actual characterized MYOC shorter forms, as follows:
3.1 The generation, isolation and characterization of full-length and all shorter forms of the MYOC cDNA (i.e. 1.1 to 1.4 above, followed by the cloning and characterization of the cDNA clones by DNA sequencing).
3.2 The 'library' of cDNA clones (i.e. the plasmid nucleic acid of each clone, or just the insert nucleic acid of each clone) are applied onto a solid support (for example glass, nylon membrane) at high density in a grid-like array (this constitute the cDNA microarray), by spotting, or 'printing' or other techniques well known in the art, followed by the immobilization of the cDNAs on the support.
3.3 The cDNA microarrays (identical copies of the microarray having being made in 3.2) are hybridized with single stranded cDNA probes that are derived from the mRNA isolated from the individual under investigation (as outlined in 1.1 to 1.3). The probes are radioactively labeled, and the signals are visualized by autoradiography, but other detection methods may also be used (i.e. non-radioactive labels, such as fluorescent labels or enzymatic labels). 3.4 The hybridization and the subsequent washing steps are performed to provide a high level of stringency so that incompletely hybridized probes will be unstable and will not give rise to a detectable signal. Thus, a nucleic acid probe hybridizing with a non- identical nucleic acid on the microarray will not result in a hybrid or duplex formation.
3.5 The resulting pattern and level of hybridization (i.e. the transcriptional profile) may then be compared to the pattern profile from a control (i.e. non-diseased individual).
The information provided by the pattern profile [i.e. the location of the 'dots', the number of dots, the intensity (or color in the case of a fluorescent or colorimetric label) of each individual 'dots'] may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have the disease. Prior calibration of this methodology with known diseased and non-diseased subjects is required.
A variation of the cDNA microarray is the polypeptide microarray to detect protein expression. Here, epitope-specific antibodies of myocilin are immobilized on the microarray, and hybridized or interacted with the pool of target, labeled polypeptides, derived from the individual under investigation. The resulting translational profile is then analysed as for the transcriptional profile in 3.5 above; used in a statistical calculation to determine the probability that the individual under investigation may or may not have the disease. Prior calibration of this methodology with known diseased and non-diseased subjects is required. Terms and terminology used in conjunction with the invention are known in the art.
5.2. Fabricaton of microarrays and uses thereof. 5.2.1. Fabrication.
The invention includes methodologies for forming an array, preferably a microarray, of analyte-assay regions on a solid support, where each region has a known amount of a selected, analyte-specific reagent. The methodologies may be used in forming a multitude of such arrays or microarrays. In one aspect, the invention includes a solid support with a surface (for instance, a glass surface, nylon, etc.) having an array of 10 or more, preferably 50 or more, preferably 250 or more, distinct polynucleotide (single-stranded) or polypeptide biopolymers per cm2 surface area. Each distinct biopolymer (a) is positioned at a separate, defined location in said microarray, (b) has a length of 10 or more monomer units, preferably 30 or more monomer units, more preferably 90 or more monomer units, and (iii) is disposed in a defined amount in the range of about 0.1 femtomoles to 200 nanomoles. In one embodiment, the biopolymers are macromolecules, either MYOC nucleic acids or proteins, and are from a vertebrate. In a preferred embodiment, the biopolymers are either MYOC nucleic acids or proteins, and are from a mammal, for example a human. In a more preferred embodiment, the biopolymers are either MYOC nucleic acids or polypeptides, and has the sequence set forth in SEQ ID No. 1, 2, 3, or figure 4, or a complement thereof (if nucleic acids), or a portion thereof. In an even more preferred embodiment, PCR-based methodologies are used to amplify the wild type and shorter MYOC nucleic acids from cells that originated from a human subject. These amplified MYOC fragments are then converted into single-stranded polynucleotides for fabrication onto a microarray. The MYOC nucleic acids are converted into polynucleotides by isolating the individual amplified fragments from a mixture of fragments in a PCR-based amplification product, followed by the immobilization of these isolated fragments (or clones, or subclones thereof) onto a microarray by means well known to a skill artisan.
The invention includes a wide variety of methodologies for the fabrication of ordered microarrays of macromolecules on a surface of a support. Herein, the term "support" shall include but not limited to, a porous or non-porous membrane, a polyacrylamide layer, a substrate, a glass or microscope slide, etc. By way of illustration, and without a limitation of scope, the following is a list of examples:
One methodology is the use of the "dot blot" approach where the nucleic acid is immobilized on the porous membrane by baking the membrane or exposing it to UV radiation. Another methodology utilizes an array of pins dipped into the wells (for instance, the 96 wells of a microtitre plate) for transferring an array of samples to a support. The array may be made employing pins that are designed to spot a surface of the support in a staggered manner (Lehrach, et al., 1990). An ordered microarray of nucleic acids may also be made using elaborate synthetic schemes to synthesize different nucleic acid sequences at different discreet regions of a support [e.g. Pirrung, et. al. (1992), and Fodor, et. al. (1991), Southern, et. al. (1992)]. Another methodology [Khrapko, et. al.(1991)] creates an oligonucleotide matrix, either manually or by automation, by spotting DNA onto a support. In addition, the current invention includes technologies for performing nucleic acid hybridization to the above, fabricated microarrays [for example, by sealing the support in a plastic bag (Maniatas, et. al. (1989) or a rotating (e.g. glass) cylinder (Robbins Scientific) with the labeled hybridization probe inside the sealed container]. For ordered microarrays of a non-porous surface (e.g. a glass or microscope slide), the array is incubated with the labeled hybridization probe sealed under a coverslip, or a small chamber.
The invention also includes methodologies for printing antibodies onto microarrays for screening MYOC polypeptides. For instance, Abouzied, et. al. (1994) devised a method of printing horizontal lines of antibodies on a nitrocellulose membrane and separating areas of the membrane with vertical hydrophobic stripes of material. A variation of this methodology prints MYOC polypeptides onto microarrays (as used herein, an antibody may be a polypeptide, but a polypeptide may not necessarily be an antibody) . Also within the scope of the invention, is the use of these antibody/polypeptide microarrays for the diagnostic and screening applications outlined in the specification.
5.2.2. Examples of use.
One embodiment of the invention is a methodology for assaying and detecting the differential expression of each of a plurality of MYOC polynucleotides in a first cell type, with respect to expression of the same polynucleotides in a second cell type. The two cell types could represent cells from two different subjects (for instance, a normal subject and a diseased subject), or representing cells derived from two different tissues from the same individual, or representing samples of the same tissue taken at different times of the same individual. In performing the methodology, fluorescent-labeled (other detectable labels may also be used) cDNAs derived from mRNAs isolated from the two cell types is first produced, where the cDNAs from the first and second cell types are labeled with first and second different fluorescent reporters, respectively. A mixture of the labeled cDNAs from the two cell types is added to the microarray of polynucleotides representing a plurality of MYOC sequences derived from the two cell types, under conditions that allows the hybridization of the cDNAs to the complementary, immobilized polynucleotides in the microarray. Fluorescence examination of the microarray under excitation conditions in which (a) polynucleotides of the microarray that hybridized predominantly to cDNAs from one of the first or second cell types give a distinct first or second fluorescence emission color, respectively, and (b) polynucleotides hybridized to approximately equal numbers of cDNAs from the first and second cell types give a distinct combined fluorescence emission color, respectively. The relative expression of each MYOC sequence in the two cell types can then be measured by the observed fluorescence emission color of each region in the mircoarray. A variation of the above methodology employs one identical microarray for each cell type studied. In performing the methodology, radioactively labeled (other detectable labels may also be used, for instance enzymatic labels) cDNAs derived from mRNAs isolated from the first cell type is first produced. The mixture of labeled cDNAs is then added to the polynucleotides immobilized on the microarray, under conditions, which will allow hybridization of the cDNAs to the complementary polynucleotides of the microarray. Examination of the resulting autoradiograph after suitably exposing the microarray to an appropriate film will allow the expression profile of the MYOC polynucleotides and the level of expression of each individual polynucleotide member to be determined. The methodology is then repeated for the second cell type, etc. The MYOC expression profile of the different cell types are then compared and analyzed. Variations of the above include colorimetric or fluorescent means of detection. Other features and variations of this aspect of the invention concerning the methods of fabricating microarrays of biological samples, and the generation of biopolymers for fabricating onto a microarray, and their uses thereof will be apparent to one who is skilled in the art, are also included herein.
5.2.3. Diagnostic applications
The ability to form high-density microarrays where each region is formed of a well- defined amount of deposited and immobilized nucleic acid sequences can be employed for large scale hybridization assays in numerous genetic applications, including medical diagnosis.
To illustrate the use for genetic diagnosis, a microarray containing multiple polynucleotide forms of MYOC (wild type and deleted shorter forms) can be probed with a labeled mixture of a patient's cDNAs (derived from the isolated mRNAs), which will specifically hybridizes with those complementary immobilized single-stranded polynucleotides on the microarray. The detection of these interactions can lead to medical prognosis and/or diagnosis with respect to Glaucoma, Retinal degenerative diseases and cardiovascular diseases. Other molecules of genetic interest, such as RNAs, can be immobilized on the microarray or alternately used as the labeled probe mixture that is applied to the microarray.
By way of illustration and without a limitation of scope, total cDNA derived from a normal cell (from sample of control subject) is labeled with one color fluorophore and total cDNA derived from a diseased cell (from sample of diseased subject) with another color fluorophoere and simultaneously hybridizing the two cDNA populations to the same microarray of cDNA polynucleotides allows for differential gene expression to be measured as the ratio of the two fluorophore intensities. This two-color experiment can be used to monitor gene expression in different disease states, tissue types, response to drugs, or response to other treatments/therapies. Such a procedure can be employed to screen many patients or individuals against all known forms or mutations of the MYOC gene. The assay format can be reversed where the patient nucleic acids is immobilized as the microarray elements and each microarray is hybridized with a different mutated allele, or genetic forms.
In addition to the above applications, microarrays of whole cells, peptides, enzymes, antibodies, antigens, receptors, ligands, phospholipids, polymers, drug cogener preparations or chemical substances can be fabricated by the means described in the invention for large scale screening assays in medical diagnostics, drug discovery, toxicology and molecular biology.
Included within the scope of the invention is the use of microarrays for performing mass screening for diagnostic applications. For example, numerous microarrays can be fabricated on the same solid support and each microarray reacted with a different population of nucleic acid or polypeptide (in the case of the polypeptide microarrays) probe while the solid support is processed as a single sheet of material.
5.3. Identifying MYOC therapeutics.
The invention provides screening assays such as cell-free assays, cell-based assays and transgenic animals, for the purpose of identifying therapeutics that are useful in the treatment of the disease or for the prevention of the disease.
5.3.1. Cell-free assays.
Cell-free assays can be used to identify MYOC therapeutics which can interact with a MYOC protein, or a MYOC protein binding partner (MPBP), and/or which can modify one or more activities of a MYOC protein or a MPBP.
An illustrative cell-free assay includes the steps of (i) forming a reaction mixture of (a) a MYOC protein or a functional fragment thereof, (b) a MPBP or a functional fragment thereof (c) a test compound or a library of test compounds, and (ii) detecting the interaction of the molecules in the assay and/or (iii) detecting the alteration in one or more activities of the MYOC protein (or a functional fragment thereof) or the MPBP (or a functional fragment thereof). The detection of interacting molecules (i.e. complex formation), the quantitation of a modulation of the complex formation, or the quantitation of one or more activities of the interacting molecules (i.e. reactants), may use a radiolabeled, a fluorescently labeled, or enzymatically labeled reactant. Alternatively, immunodetection may be employed using antibodies directed against one or more of the reactants. In addition, the protein to be detected in the complex can be "epitope tagged" in the form of a fusion protein (e.g. a GST-fusion protein). In a preferred embodiment, the MYOC protein or its binding partner is immobilized on a support matrix (e.g. by conjugation to biotin or streptavidin) to aid in the separation of the complexes from the uncomplexed molecules, and to enable automation of the assay.
5.3.2. Cell-based assays
The invention also provides cell-based assays for identifying small molecule therapeutics of myocilin which may be an agonist or antagonist. Cell-based assays can be used to identify compounds, which can alter or modulate the expression of the MYOC gene, modulate the translation of one or more MYOC mRNA species, or alter the stability of one or more MYOC mRNA species or polypeptides. In one embodiment, a test compound is added to cells capable of expressing the MYOC gene, and the presence of one or more mRNA species or polypeptide is then determined and quantitated (e.g. released of protein into cell medium), and compared to that of control cells not exposed to the test compound. In addition, the specificity of the test compound for MYOC can be confirmed by analyzing the expression of one or more control genes (e.g. β-actin gene).
In an preferred embodiment, the effect of the test compound on the expression of the MYOC gene at the transcriptional level can be determined with the use of a reporter construct whereby the promoter (or a portion thereof) of the MYOC gene is operatively linked to a reporter sequence, whose gene product can be readily quantifiable (e.g. β- galactosidase, or luciferase). Such reporter gene, as also the methods for isolating the promoter region from a genomic library, is well known to one who is skilled in the art.
5.3.3. Transgenic Animals
The invention provides for transgenic non-human animals, which can be used for a number of purposes, and the following is not meant to be an exhaustive list: a) To identify MYOC therapeutics b) Using "knock-out" transgenic animals to determine the function of MYOC, the phenotype of a MYOC knock-out animal, and to identify genes which affect the animal's susceptibility to the disease. c) Using transgenic animals harboring a MYOC promoter/reporter gene transgenic construct to identify compounds, which alter or modulate MYOC expression. d) To screen for drugs that alleviate or attenuate the disease or symptoms of the disease.
Transgenic animals of the invention include those harboring a heterologous MYOC gene or fragment thereof, or a reporter gene, under the control of the MYOC promoter or a heterologous promoter. It also includes animals whose endogenous MYOC gene has been "knock-out" (i.e. an animal carrying a heterozygous or homozygous deletion of the MYOC gene).
Also included are variations of the above, for example, the generation of "kock-in" transgenic animals. Like a knock-out construct, a knock-in construct, will contain the necessary sequences required for homologous recombination, a positive selectable marker, but NO omission of the coding sequences. In addition, to select against non- homologous recombination events, the knock-out and knock-in constructs are flanked by negative selectable markers at either end (e.g. through the use of two allelic variants of the thymidine kinase gene, and incorporating a drug like 5-bromodeoxyuridine into the culture medium).
Methods for generating transgenic or "knock-out" animals are well known in the art. For example, gene targeting in embryonic stem cells (ES cells) can be performed with a transgenic construct designed to undergo homologous recombination with the corresponding genomic sequences, which provides a positive selection trait (e.g. neomycin resistance) in the process. In an illustrative embodiment, either the FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al. (1991) Science, 251, 1351-1355) or the cre/loxP recombinase system of bacteriophage PI (e.g. see Orban et al. (1992) PNAS 89, 6232-6236) can be used to create in vivo site-specific genetic recombination systems. The required ES cells are generated and maintained using methods well known to the skilled artisan (for example, see Doetschman et al. (1985) J. Embryol. Exp. 87, 27-45). Once suitable ES cells containing the transgene/transgenic construct in the correct location can be identified by the selection techniques described above, the cells can be inserted into the embryo using techniques well known to the skilled artisan (e.g. electroporation, lipofection), preferably by microinjection. The offspring of the foster mother can be screened using a number of methodologies available. For example, they may be screened using Southern blot or PCR (using for example, DNA extracted from tail tissue), or screened for mosaic coat color (if the coat selection strategy is used), or by Northern blots (looking for expression of the gene knocked out or the marker gene or both), or by Western blots (using antibodies directed at the transgene or marker gene's translation product). The skilled artisan, to introduce specific transgene sequences into organisms utilizing methods and materials well known in the art, can adapt this general description for the generation of transgenic animals.
The transgene can be the wild type form of the protein, or variants thereof, or portion thereof, or homologs thereof, agonists or antagonists thereof, or antisense constructs thereof. In a preferred embodiment, the expression of the transgene is restricted to certain cells, tissues or developmental stages of the animal, using for example, cis-acting elements that controls the expression in the pattern desired.
Generating and analyzing the transcriptional and translational profiles of myocilin may identify therapeutics for the treatment of the disease. In one embodiment, the screening assays to identify drug candidates will comprise the following steps:
(a) Extracting a preadministration sample from a patient before the administration of the drug.
(b) Deriving the transcriptional profile and the translational profile of MYOC of the sample.
(c) Administration of the drug.
(d) Extracting one or more postadministration sample from the individual
(e) Deriving the transcriptional and translational profiles from the postadministration sample(s).
(f) Comparing the profiles from the preadministration sample with the profiles from the postadministration sample(s).
5.4. Pharmacogenomics.
In another embodiment, the above screening assays may be adapted for the use of pharmacogenomics. The customization of the treatment for a particular disease according to the genetic profile of an individual is the basis of pharmacogenomics.
The information gathered on the nature of the genetic defect (MYOC genetic profile), as determined from the transcriptional and translational profiles of MYOC, may be used alone, or in conjunction with information on other defects contributing or causing the same disease (disease genetic profile). The goal of pharmacogenomics is to permit the selection of drugs or the design of drug treatment that are not only expected to be effective, but also, to be safe for a particular patient or patient population (i.e. a group of patients having the same genetic defect or profile).
Therefore, the transcriptional and translational profiles may be used to monitor the effectiveness of a drug/therapeutic treatment. This will determine whether the treatment is effective or whether it should be altered and optimized. The scope of the invention is extended to include the monitoring of drug effectiveness in clinical trials. In one embodiment, the method of determining the effectiveness of the drug candidate (identified using the screening assays described above) comprise the following steps:
(a) Extracting a preadministration sample from a patient before the administration of the drug.
(b) Deriving the transcriptional profile and the translational profile of MYOC of the sample.
(c) Administration of the drug.
(d) Extracting one or more postadministration sample from the individual.
(e) Deriving the transcriptional and translational profiles from the postadministration sample(s).
(f) Comparing the profiles from the preadministration sample with the profiles from the postadministration sample(s).
(g) Adjusting the administration of the drug candidate, or selection of an alternative drug candidate, to the patient accordingly.
The invention includes the novel drugs/therapeutics identified using the assays described above and their uses thereof for the prevention and treatment of the disease. 5.5 Other human genetic diseases and their genetically linked genes.
By way of illustration, and without a limitation of scope, the specification of the invention has been written for MYOC as the linkage gene (or susceptibility gene), and
Glaucoma, retina degenerative diseases and cardiovascular diseases, as the genetic diseases.
Therefore, the scope of the current invention includes the application of the above specification to any gene or genes and the corresponding human genetic diseases whereby the said gene or genes has been found to be genetically linked to the said human genetic diseases. The following set of linkage gene(s)/genetic diseases(s) are therefore also included within the scope of the invention.
Genetic diseases Gene s)
1. Bardet-Biedl syndrome (BBS) BBS2, BBS4, and BBS6
2. Crohn's disease NOD2
3. Late-onset type 2 diabetes MODY2
4. Darier disease ATP2A2
5. Ulcerative Colitis MUC3
6. Hypertrophic cardiomyopathy Troponin T
7. Late-onset familial cardiac hypertrophy Myosin binding protein C
8. Hailey-Hailey disease ATP2C1 8. Alzheimer's disease Genes encoding for: Presenilin 1,
Presenilin 2, and Amyloid Precursor protein.
Although the invention has been described with respect to specific embodiments and methods, it will be clear that various changes and modification may be made without departing from the invention.
This Disclosure Document #479362 filed on September 7th 2000 precedes this application and is reproduced here for full and complete inclusion:
Fingerprinting techniques to diagnosis people with glaucoma.
Three main methodologies are disclosed for the generation of a genetic profile (i.e. 'fingerprint') based on the expression of both the wild type (i.e. full length) and shorter (either with a deletion or truncation) forms of the Trabecular meshwork Inducible Glucocorticoid Responsive protein (MYOC), also called myocilin (MYOC), and their messenger ribonucleic acids (mRNAs):
1. The detection of the full-length and shorter forms of the MYOC mRNA or the complementary Deoxyribonucleic acid (cDNA) that are derived from it.
2. The detection of the full-length and shorter forms of the MYOC protein.
3. The use of microarrays or biochips to detect (1) above.
1. The detection of the full-length and shorter forms of the MYOC cDNA/mRNA The detection of the full-length and shorter forms of the MYOC cDNA
1.1 Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or body fluids (for example Aqueous humor, Viteous humor, peripheral blood cells, urine etc.).
1.2 Isolate mRNAs from 1.1
1.3 Synthesize cDNAs (either single stranded cDNA or double stranded cDNA) from 1.2
1.4 Amplification of MYOC cDNAs by the polymerase chain reaction (PCR) using MYOC specific primers (pair, forward and reverse) whose DNA sequences are derived either from the coding [i.e. Open reading frame (ORF)] or from the non- coding regions (for example 5'-untranslated, promoter, 3 '-untranslated) of the MYOC gene, with any thermostable polymerase or related enzymes.
1.5 Separation of the PCR products from 1.4 by electrophoresis on gel-based medium (for example agarose gels).
1.6 Transfer of the separated DNA fragments by Southern transfer onto a solid support (for example nitrocellulose, nylon membranes). 1.7 Hybridization of the PCR products immobilized on the solid support with a radioactive labelled DNA or RNA probe derived from MYOC, and subsequent visualization of the hybridization signals by autoradiography. Other methods of detection may also be used (i.e. non-radioactive labels).
1.8 The genetic profile derived from 1.7 (i.e. the 'barcodes') may be compared to the genetic profile from a control (i.e. non-glaucoma individual).
The information provided by the genetic profile (i.e. the position of the bands, the number of bands, the intensity of each individual bands) may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have glaucoma. Prior calibration of this methodology with known glaucoma and non-glaucoma subjects is required.
The detection of the full-length and shorter forms of the MYOC mRNA
A modification of the methodology in (1) allow for the detection of full-length and shorter forms of the MYOC mRNA:
After 1.1 and 1.2, the mRNAs are separated as described in 1.5 but under denaturating condition (for example in formaldehyde-gel based systems). 1.6 is modified to the
Northern transfer protocol, with 1.7 and 1.8 as described above.
2 The detection of the full-length and shorter forms of the MYOC protein.
2.2 Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or body fluids (for example Aqueous humor, Viteous humor, peripheral blood cells, urine etc.).
2.3 Lyse cells and/or isolate total cellular proteins
2.4 Separation of proteins by gel electrophoresis under denaturing or non-denaturing conditions (for example SDS-PAGE, 2-D gel etc).
2.5 Transfer separated proteins from the gel medium to a solid support (for example nylon membrane) by the Western blotting protocol.
2.6 Detection of the immobilized proteins from 2.4 with single or multiple specific anti- MYOC antibodies (polyclonal or monclonal). 2.7 Visualization of the signals from 2.5 by autoradiography, as the antibodies used in 2.5 are conjugated to a radioactive label. Other methods of detection may also be used (i.e. non-radioactive labels). To enhance the sensitivity of this method, primary and secondary antibodies may be used in a sandwich-type detection assay.
2.8 The genetic profile derived from 2.6 (i.e. the 'barcodes') may be compared to the genetic profile from a control (i.e. non-glaucoma individual).
The information provided by the genetic profile (i.e. the position of the bands, the number of bands, the intensity of each individual bands) may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have glaucoma. Prior calibration of this methodology with known glaucoma and non-glaucoma subjects is required.
A modification of the methodology in (2) uses the principle of immunoprecipitation. Here, after 2.1 and 2.2, the isolated proteins are mixed and incubated with the MYOC specific antibodies prior to their separation by gel-based electrophoresis. Proteins, which are not bound to the anti-MYOC antibodies are then removed (for example using protein A). Then steps 2.5, 2.6 and 2.7 as above.
3. Hybridization to high density oligonucleotide arrays to detect expression of MYOC This invention provides methods for the characterization of the expression levels and the pattern of expression of a multiplicity of MYOC nucleic acid forms. The methods involve obtaining a sample from a subject, hybridizing the nucleic acids (either mRNAs or the cDNAs derived from it) from the sample to a high density array of nucleic acids probes (either oligonucleotides or cDNA molecules, representing naturally occurring MYOC nucleic acid forms) where the high density array contains nucleic acid probes complementary to sequences and/or subsequences of target nucleic acids in the nucleic acid sample.
In one embodiment, the method involves providing a pool of target nucleic acids (derived from a sample obtained from the subject) comprising RNA transcripts of one or more target forms, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of said nucleic acid probes immobilized on surface (for example glass, nylon etc.) where the array comprises more than 10, preferably more than 100, more preferably more than 1000, different nucleic acid probes and each different nucleic acid probe is localized in a predetermined region on the surface of the solid support microarray, the density of the different nucleic acid probes is greater than about 10, preferably greater than 50, more preferably greater than 100, per 1 cm2, and the nucleic acid probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the microarray.
In a modification of the above method, the use of the oligonucleotides on the array is substituted with nucleic acids of actual characterized MYOC shorter forms, as follows:
3.1 The isolation, generation, and characterization of full-length and all shorter forms of the MYOC cDNA (i.e. 1.1 to 1.4 above, followed by the cloning and characterization of the cDNA clones by DNA sequencing).
3.2 The 'library' of cDNA clones are applied onto a solid support (for example glass, nylon memebrane) at high density in a grid-like array (this constitute the cDNA microarray), by spotting, or 'printing' or other techniques well known in the art, followed by the immobilization of the cDNAs on the support.
3.3 The cDNA microarrays (identical copies of the microarray having being made in 3.2) are hybridized with single stranded cDNA probes that are derived from the mRNA isolated from the individual under investigation (as outlined in 1.1 to 1.3). The probes are radioactively labelled, and the signal are visualized by autoradiography, but other detection methods may also be used (i.e. non-radioactive labels used).
3.4 Hybridization and the subsequent washing steps are performed to provide a high level of stringency so that incompletely hybridized probes will be unstable and will not give rise to a detectable signal.
5.5 The resulting pattern of hybridization may then be compared to the pattern profile from a control (i.e. non-glaucoma individual).
The information provided by the pattern profile (i.e. the location of the 'dots', the number of dots, the intensity of each individual dots) may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have glaucoma. Prior calibration of this methodology with known glaucoma and non- glaucoma subjects is required.
Terms and terminology used in conjunction with the invention are known in the art.
This Disclosure Document #482334 filed on November 13th 2000 precedes this application and is reproduced here for full and complete inclusion:
11/13/00
Genetic profiling techniques for the diagnosis and prognosis of retinal diseases in subjects.
The present invention describes methodologies for the diagnosis/prognosis of retinal diseases in human subjects, whether the individual is asymptomatic or have clinical symptoms.
The invention makes use of the recent finding (T. H. Kong, unpublished results) that both wild type (i.e. full length) and shorter (either with deletion or truncation) forms of the Trabecular meshwork Inducible Glucocorticoid Response protein (MYOC, also called Myocilin (MYO)) and their messenger ribonucleic acids (mRNAs) are present in ocular and non-ocular tissues. More importantly, these shorter forms are differentially expressed between normal and diseased individuals.
The methodologies described herein apply to all retinal diseases and the following is not intended to be an exhaustive list. Age Related Macular Degeneration, Retinitis Pigmentosa, Usher Syndrome, Stargardt Disease, Bardet-Biedl Syndrome, Best Disease, Choroideremia, Juvenile Retinoschisis, Leber Congenital Amaurosis, Blue-Cone Monochromacy, Central Areolar Choroidal Dystrophy, Cone-Rod Dystrophy, Cone Dystrophy, Congenital Stationary Night Blindness, Dominant Drusen, Goldmann-Favre Dystrophy, Gyrate Atrophy, Kearns-Sayre Syndrome, Macular Drusen, Macular Dystrophy, Malattia Leventinese, Oguchi Disease, Refsum Disease, Atypical RP, Retinitis Punctata Albescens, Rod Dystrophy, Rod-Cone Dystrophy, Rod Monchromatism, Sector RP, Sorsby Fundus Dystrophy, Sjogren-Larsson Syndrome.
Three main methodologies are disclosed for the generation of a genetic profile (i.e. 'fingerprint') based on the expression of both the wild type (i.e. full length) and shorter (either with a deletion or truncation) forms of the Trabecular meshwork Inducible Glucocorticoid Responsive protein (MYOC), also called myocilin (MYOC), and their messenger ribonucleic acids (mRNAs):
1. The detection of the full-length and shorter forms of the MYOC mRNA or the complementary Deoxyribonucleic acid (cDNA) that are derived from it.
2. The detection of the full-length and shorter forms of the MYOC protein
3. The use of microarrays or biochips to detect (1) above.
1. The detection of the full-length and shorter forms of the MYOC cDNA mRNA The detection of the full-length and shorter forms of the MYOC cDNA
1.1 Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or body fluids (e.g. Aqueous humor, Viteous humor, blood sample, urine etc.).
1.2 Isolate mRNAs from 1.1
1.3 Synthesize cDNAs (either single stranded cDNA or double stranded cDNA) from 1.2
1.4 Amplification of MYOC cDNAs by the polymerase chain reaction (PCR) using MYOC specific primers (pair, forward and reverse) whose DNA sequences are derived either from the coding [i.e. Open reading frame (ORF)] or from the non- coding regions (e.g. 5 '-untranslated, promoter, 3 '-untranslated) of the MYOC gene, with any thermostable polymerase or related enzymes.
1.5 Separation of the PCR products from 1.4 by electrophoresis on gel-based medium (e.g. agarose gels).
1.6 Transfer of the separated DNA fragments by Southern transfer onto a solid support (e.g. nitrocellulose, nylon membranes).
1.7 Hybridization of the PCR products immobilized on the solid support with a radioactive labelled DNA or RNA probe derived from MYOC, and subsequent visualization of the hybridization signals by autoradiography. Other methods of detection may also be used (i.e. non-radioactive labels).
1.8 The genetic profile derived from 1.7 (i.e. the 'barcodes') may be compared to the genetic profile from a control (i.e. normal individual). The information provided by the genetic profile (i.e. the position of the bands, the number of bands, the intensity of each individual bands) may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have a retinal disease. Prior calibration of this methodology with individuals known to have the disease and non-diseased subjects is required.
The detection of the full-length and shorter forms of the MYOC mRNA
A modification of the methodology in (1) allow for the detection of full-length and shorter forms of the MYOC mRNA:
After 1.1 and 1.2, the mRNAs are separated as described in 1.5 but under denaturating condition (e.g. in formaldehyde-gel based systems). 1.6 is modified to the Northern transfer protocol, with 1.7 and 1.8 as described above.
2. The detection of the full-length and shorter forms of the MYOC protein.
2.1 Either of an ocular or non-ocular origin from the human body where MYOC is known to be expressed - isolate tissues, cells or body fluids (e.g. Aqueous humor, Viteous humor, blood sample, urine etc.).
2.2 Lyse cells and/or isolate total cellular proteins
2.3 Separation of proteins by gel electrophoresis under denaturing or non-denaturing conditions (e.g. SDS-PAGE, 2-D gel etc).
2.4 Transfer separated proteins from the gel medium to a solid support (e.g. nylon membrane) by the Western blotting protocol.
2.5 Detection of the immobilized proteins from 2.4 with single or multiple specific anti-MYOC antibodies (polyclonal or monclonal).
2.6 Visualization of the signals from 2.5 by autoradiography, as the antibodies used in 2.5 are conjugated to a radioactive label. Other methods of detection may also be used (i.e. non-radioactive labels). To enhance the sensitivity of this method, primary and secondary antibodies may be used in a sandwich-type detection assay.
2.7 The genetic profile derived from 2.6 (i.e. the 'barcodes') may be compared to the genetic profile from a control (i.e. normal individual). The information provided by the genetic profile (i.e. the position of the bands, the number of bands, the intensity of each individual bands) may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have a retinal disease. Prior calibration of this methodology with individuals known to have the disease and non-diseased subjects is required.
A modification of the methodology in (2) uses the principle of immunoprecipitation. Here, after 2.1 and 2.2, the isolated proteins are mixed and incubated with the MYOC specific antibodies prior to their separation by gel-based electrophoresis. Proteins, which are not bound to the anti-MYOC antibodies are then removed (e.g. using protein A). Then steps 2.5, 2.6 and 2.7 as above.
3. Hybridization to high density oligonucleotide arrays to detect expression of MYOC This invention provide methods for the characterization of the expression levels and the pattern of expression of a multiplicity of MYOC nucleic acid forms. The methods involve obtaining a sample from a subject, hybridizing the nucleic acids (either mRNAs or the cDNAs derived from it) from the sample to a high density array of nucleic acids probes (either oligonucleotides or cDNA molecules, representing naturally occurring MYOC nucleic acid forms) where the high density array contains nucleic acid probes complementary to sequences and/or subsequences of target nucleic acids in the nucleic acid sample.
In one embodiment, the method involves providing a pool of target nucleic acids (derived from a sample obtained from the subject) comprising RNA transcripts of one or more target forms, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of said nucleic acid probes immobilized on surface (e.g. glass, nylon etc.) where the array comprises more than 10, preferably more than 100, more preferably more than 1000, different nucleic acid probes and each different nucleic acid probe is localized in a predetermined region on the surface of the solid support microarray, the density of the different nucleic acid probes is greater than about 10, preferably greater than 50, more preferably greater than 100, per 1 cm2, and the nucleic acid probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the microarray.
In a modification of the above method, the use of the oligonucleotides on the array is substituted with nucleic acids of actual characterized MYOC shorter forms, as follows:
3.1 The isolation, generation, and characterization of full-length and all shorter forms of the MYOC cDNA (i.e. 1.1 to 1.4 above, followed by the cloning and characterization of the cDNA clones by DNA sequencing).
3.2 The 'library' of cDNA clones are applied onto a solid support (e.g. glass, nylon memebrane) at high density in a grid-like array (this constitute the cDNA microarray), by spotting, or 'printing' or other techniques well known in the art, followed by the immobilization of the cDNAs on the support.
3.3 The cDNA microarrays (identical copies of the microarray having being made in 3.2) are hybridized with single stranded cDNA probes that are derived from the mRNA isolated from the individual under investigation (as outlined in 1.1 to 1.3). The probes are radioactively labelled, and the signal are visualized by autoradiography, but other detection methods may also be used (i.e. non-radioactive labels used).
3.4 Hybridization and the subsequent washing steps are performed to provide a high level of stringency so that incompletely hybridized probes will be unstable and will not give rise to a detectable signal.
3.5 The resulting pattern of hybridization may then be compared to the pattern profile from a control (i.e. normal individual).
The information provided by the pattern profile (i.e. the location of the 'dots', the number of dots, the intensity of each individual dots) may be used in a statistical calculation to determine the probability that the individual under investigation may or may not have a retinal disease. Prior calibration of this methodology with individuals known to have the disease and normal subjects is required.
Terms and terminology used in conjunction with the invention are known in the art.

Claims

What is claim is:
1. A method for determining whether a subject has or is at risk of developing a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease, comprising of generating a transcriptional profile (i.e. a 'fingerprint') in the subject or in a sample obtained from the subject, based on the expression of the different MYOC mRNA species, wherein a difference in the profile relative to that in a normal subject indicates that the subject has or is at risk of developing a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease.
2. A method as claimed in claim 1, wherein the sample obtained from the subject is used to generate a reverse transcription (RT) reaction.
3. A method as claimed in claims 1 or 2, wherein the cDNAs of the RT are amplified by the polymerase chain reaction (PCR) or PCR-based techniques.
4. A method as claimed in any of the claims 1 to 3 in which the products of the amplification are separated, immobilized and hybridized with one or more MYOC polynucleotide probe(s).
5. A method as claimed in any of the claims 1 to 4 in wherein said polynucleotide probe(s) includes a labeled group attached thereto, which is capable of being detected.
6. A method as claimed in any of the claims 1 to 5, wherein said polynucleotide probe(s) consists of a sequence derived from any part or whole of the MYOC gene.
7. A method for determining whether a subject has or is at risk of developing a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease, comprising of generating a translational profile in the subject or in a sample obtained from the subject, based on the expression of the different MYOC polypeptide forms, wherein a difference in the profile relative to that in a normal subject indicates that the subject has or is at risk of developing a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease.
8. A method as claimed in claim 7, wherein a pool of polypeptides is derived from the sample obtained from the subject.
9. A method of claim 7 or 8, wherein the said pool of MYOC polypeptides is separated and immobilized, and characterized (i.e. qualified and quantified) in an immunoassay using one or more antibodies.
10. A method as claimed in any of the claims 1 to 4 in wherein said antibodies include a labeled group attached thereto, which is capable of being detected.
11. A method of claim 1, wherein the novel nucleic acid and protein forms of MYOC are detected using a detection technique selected from the group consisting of Northern blot analysis, dot blot analysis, polymerase chain reaction (PCR), reverse transcription PCR (RT-PCR), anchor PCR, RACE PCR, ligase chain reaction (LCR), in situ hybridization, immunoprecipitation, Western blot analysis, immunochemistry, Genetic bit analysis, primer guided nucleotide incoφoration, oligonucleotide ligation assay (OLA), protein truncation test (PTT) and other hybridization-based techniques.
12. A method for establishing a MYOC genetic population profile in a population of individuals having a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease, comprising determining a MYOC genetic profile of the individuals in the population and establishing a relationship between the MYOC genetic profiles and specific characteristics of the individuals.
13. The method of claim 12, wherein the specific characteristics of the individual include the individual's response to treatment.
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14. A method for pharmacogenomically selecting a therapy to administer to an individual having a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease, comprising determining a MYOC genetic profile of an individual and comparing the individual's MYOC genetic profile to a MYOC genetic population profile, to thereby select a therapy for administration to the individual.
15. The method of claim 14, wherein determining the MYOC genetic profile of an individual comprises determining a transcriptional profile and a translational profile of MYOC, and/or determining the identity of any single nucleotide polymoφhisms (SNP).
16. A kit for determining whether a subject has or is likely to develop a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease, comprising a probe or primer, which hybridizes to a MYOC nucleic acid and instructions for use.
17. The kit of claim 16, wherein the probe further includes a label group attached thereto, which is capable of being detected.
18. The kit of claim 16, wherein the probe or primer comprises at least about 12 consecutive nucleotides of sense or anti-sense sequence selected from the group consisting of SEQ ID NO.l, SEQ ID NO.3 and naturally occurring mutants thereof.
19. A method for determining whether a subject has or is at risk of developing a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease, comprising of obtaining a sample from the subject, characterizing the subject's pattern of MYOC nucleic acid forms and their expression levels using a high density nucleic acid microarray, wherein a difference in the pattern and/or levels relative to that in a normal subject indicates that the subject has or is at risk of developing a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease.
20. A method as claimed in claim 19, wherein a pool of MYOC nucleic acids (mRNAs or cDNA molecules) is derived from the sample obtained from the subject.
21. A method as claimed in any of the claims 19 or 20 wherein said pool of nucleic acids include a labeled group attached thereto, which is capable of being detected.
22. A method as claimed in claims 19 to 21, wherein said pool of nucleic acids is used to hybridize with a high density nucleic acid microarray, where a less than 100% sequence match is indicated by an absence of hybrid formation.
23. A method as claimed in any of the claims 19 to 22, wherein the microarray consists of nucleic acid probes (either oligonucleotides or single-stranded cDNA molecules) representing naturally occurring nucleic acid forms of MYOC.
24. A method as claimed in any of the claims 19 to 23, wherein the said nucleic acid probes are immobilized on a solid support.
25. A method as claimed in any of the claims 19 to 24, wherein each of the nucleic acid probes is localized in a predetermined region on the microarray.
26. A method as claimed in any of the claims 19 to 25, wherein the density of the said nucleic probes in the microarray is 10 or higher, preferably 50 or higher, more preferably 250 or higher per cm2.
27. A method as claimed in any of the claims 19 to 26, wherein the number of said nucleic acid probes on the microarray is 50 or higher, preferably 500 or higher, more preferably 5000 or higher.
28. A method for determining whether a subject has or is at risk of developing a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease, comprising of obtaining a sample from the subject, characterizing the subject's pattern of MYOC polypeptide forms and their expression levels using a high density polypeptide microarray, wherein a difference in the pattern and/or levels relative to that in a normal subject indicates that the subject has or is at risk of developing a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease.
29. A method as claimed in claim 28, wherein a pool of MYOC polypeptides is derived from the sample obtained from the subject.
30. A method as claimed in any of the claims 28 or 29 wherein said pool of polypeptides includes a labeled group attached thereto, which is capable of being detected.
31. A method as claimed in claims 28 to 30, wherein said pool of MYOC polypeptides is used to interact directly or via a secondary antibody as in a sandwich assay, with a high density polypeptide (i.e. anti-MYOC specific antibodies) microarray.
32. A method as claimed in any of the claims 28 to 31, wherein the said polypeptide/antibody probes are immobilized on a solid support.
33. A method as claimed in any of the claims 28 to 32, wherein each of the said polypeptide/antibody probes is localized in a predetermined region on the microarray.
34. A kit for determining whether a subject has or is likely to develop a glaucoma disease, a retinal degenerative disease, or a cardiovascular disease, comprising a antibody or peptide probe, which is capable of specifically binding to the novel MYOC polypeptide(s) and instructions for use.
35. The kit of claim 34, wherein the said probe further includes a label group attached thereto, which is capable of being detected.
36. The kit of claim 34, wherein the probe comprises about 10 consecutive amino acid residues or more selected from the group consisting of SEQ ID NO.2, and naturally occurring mutants thereof.
PCT/US2001/048622 2001-04-04 2001-12-11 Diagnostics and therapeutics for glaucoma, retinal degenerative diseases and cardiovascular diseases based on novel nucleic acids and protein forms of myocilin (myoc) WO2002082969A2 (en)

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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
RU2694744C1 (en) * 2018-12-18 2019-07-17 Федеральное государственное бюджетное образовательное учреждение дополнительного профессионального образования "Российская медицинская академия непрерывного профессионального образования" Министерства здравоохранения Российской Федерации (ФГБОУ ДПО РМАНПО Минздрава России) Method for prediction of timolol treatment effectiveness of primary open-angle glaucoma
WO2020118293A3 (en) * 2018-12-07 2020-07-23 Georgia Tech Research Corporation Antibodies that bind to natively folded myocilin

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2020118293A3 (en) * 2018-12-07 2020-07-23 Georgia Tech Research Corporation Antibodies that bind to natively folded myocilin
RU2694744C1 (en) * 2018-12-18 2019-07-17 Федеральное государственное бюджетное образовательное учреждение дополнительного профессионального образования "Российская медицинская академия непрерывного профессионального образования" Министерства здравоохранения Российской Федерации (ФГБОУ ДПО РМАНПО Минздрава России) Method for prediction of timolol treatment effectiveness of primary open-angle glaucoma

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