Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G01N33/57407—Specifically defined cancers
  • G01N33/57449—Specifically defined cancers of ovaries
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
  • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
• • 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
  • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
• • 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
  • C12Q2600/156—Polymorphic or mutational markers
• • 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
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2500/00—Screening for compounds of potential therapeutic value
  • G01N2500/04—Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

• the invention relates to the identification of nucleic acid and protein expression profiles and nucleic acids, products, and antibodies thereto that are involved in lung cancer; and to the use of such expression profiles and compositions in diagnosis and therapy of lung cancer.
• the invention further relates to methods for identifying and using agents and/or targets that inhibit lung cancer or related conditions.
• Lung cancer is the second most commonly occurring cancer in the United States and is the leading cause of cancer-related death. It is estimated that there are over 160,000 new cases of lung cancer in the United States every year. Of those who are diagnosed with lung cancer, 86 percent will die within five years. Lung cancer is the most common visceral cancer in men and accounts for nearly one third of all cancer deaths in both men and women. In fact, lung cancer accounts for 7% of all deaths, due to any cause, in both men and women.
• Smoking is the primary cause of lung cancer, with more than 80% of lung cancers resulting from smoking.
• About 400 to 500 separate gaseous substances are present in the smoke of a non-filter cigarette.
• the most noteworthy substances include nitrogen oxides, hydrogen cyanide, formaldehyde, benzene, and toluene.
• the particles present in cigarette smoke contain at least 3,500 individual compounds such as nicotine, tobacco alkaloids (nornicotine, anatabine, anabasine), polycyclic aromatic hydrocarbons (e.g., benzo(a)pyrene, B(a)P), naphthalenes, aromatic amines, phenols, and tobacco-specific nitrosamines.
• Tobacco-specific nitrosamines are formed during tobacco curing and processing, and are suspected of causing lung cancer in humans.
• the tobacco-specific nitrosamine known as NNK produces lung adenomas and lung adenocarcinomas.
• the tobacco-specific nitrosamine known as NNAL also produces lung adenocarcinomas in rodents.
• lung cancer In addition to smoking, other factors thought to be causes of lung cancer include on- the-job exposure to carcinogens such as asbestos and uranium, exposure to chemical hazards such as radon, polycyclic aromatic hydrocarbons, chromium, nickel, and inorganic arsenic, genetic factors, and diet.
• carcinogens such as asbestos and uranium
• chemical hazards such as radon, polycyclic aromatic hydrocarbons, chromium, nickel, and inorganic arsenic, genetic factors, and diet.
• Histological classification of various lung cancers define the types of cancer that begin in the lung. See, e.g., Travis, et al. (1999) Histological Typing of Lung and Pleural Tumours (International Histological Classification of Tumours, No 1.
• Four major cell types make up more than 88% of all primary lung neoplasms. These are: squamous or epidermoid carcinoma, small cell (also called oat cell) carcinoma, adenocarcinoma, and large cell (also called large cell anaplastic) carcinoma. The remainder include undifferentiated carcinomas, carcinoids, bronchial gland tumors, and other rarer types.
• the various cell types have different natural histories and responses to therapy, and, thus, a correct histologic diagnosis is the first step of effective treatment.
• SCLC Small cell lung cancer
• Non-small cell lung cancers are the more frequently occurring form of lung cancer. They comprise squamous cell carcinoma, adenocarcinoma, and large cell carcinoma and account for more than 75% of all lung cancers. Non-small cell tumors that are localized at the time of presentation can sometimes be cured with surgery and/or radiotherapy, but usually are not identified until significant metastasis has occurred, which are typically not very responsive to surgical, chemotherapy, or radiation treatment..
• the screening of asymptomatic persons at high risk for lung cancer has often proven ineffective. In general, only 5 to 15 percent of lung cancer patients have their disease detected while they are asymptomatic. Of course, early detection and treatment are critical factors in the fight against lung cancer.
• the average survival rate is 49% for those whose cancer is detected early, before the cancer has spread from the lung.
• Lung cancer often spreads outside ofthe lung, and it may have spread to the bones or brain by the time it is diagnosed. While the prognosis may be better for lung cancers that are detected early, because ofthe lack ofv effective curative treatments, early detection does not necessarily alter the total death rate from lung cancer.
• methods for diagnosis and prognosis of lung cancer and effective treatment of lung cancer would be desirable. Accordingly, provided herein are methods that can be used in diagnosis and prognosis of lung cancer. Further provided are methods that can be used to screen candidate therapeutic agents for the ability to modulate, e.g., treat, lung cancer. Additionally, provided herein are molecular targets and compositions for therapeutic intervention in lung disease and other metastatic cancers.
• the present invention provides nucleotide sequences of genes that are up- and downregulated in lung cancer cells. Such genes are useful for diagnostic purposes, and also as targets for screening for therapeutic compounds that modulate lung cancer, such as antibodies.
• the methods of detecting nucleic acids ofthe invention or their encoded proteins can be used for a number of purposes. Examples include early detection of lung cancers, monitoring and early detection of relapse following treatment of lung cancers, monitoring response to therapy of lung cancers, determining prognosis of lung cancers, directing therapy of lung cancers, selecting patients for postoperative chemotherapy or radiation therapy, selecting therapy, determining tumor prognosis, treatment, or response to treatment, and early detection ofprecancerous lesions ofthe lung.
• benign or precancerous lesions include: atelectasis, emphysema, brochitis, chronic obstructive pulmonary disease, fibrosis, hypersensitivity pneumonitis (HP), interstitial pulmonary fibrosis (IPF), asthma, and bronchiectasis.
• HP hypersensitivity pneumonitis
• IPF interstitial pulmonary fibrosis
• the present invention provides a method of detecting a lung cancer- associated transcript in a cell from a patient, the method comprising contacting a biological sample from the patient with a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1 A-16.
• the sample may be contacted with a specific binding reagent, e.g., antibody.
• the polynucleotide selectively hybridizes to a sequence at least 95% identical to a sequence as shown in Tables 1A-16. In another embodiment, the polynucleotide comprises a sequence as shown in Tables 1A-16.
• the biological sample is a tissue sample, or a body fluid.
• the biological sample comprises isolated nucleic acids, e.g., mRNA.
• the polynucleotide is labeled, e.g., with a fluorescent label. In one embodiment, the polynucleotide is immobilized on a solid surface. In one embodiment, the patient is undergoing a therapeutic regimen to treat lung cancer. In another embodiment, the patient is suspected of having lung cancer. In one embodiment, the patient is a primate, e.g., a human.
• the method further comprises the step of amplifying nucleic acids before the step of contacting the biological sample with the polynucleotide.
• the present invention provides a method of monitoring the efficacy of a therapeutic treatment of lung cancer, the method comprising the steps of: (i) providing a biological sample from a patient undergoing the therapeutic treatment; and (ii) determining the level of a lung cancer-associated transcript in the biological sample by contacting the biological sample with a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1 A-16, thereby monitoring the efficacy ofthe therapy.
• the sample may be evaluated for protein, e.g., contacting the sample with an antibody.
• the method further comprises the step of: (iii) comparing the level ofthe lung cancer-associated transcript to a level ofthe lung cancer-associated transcript in a biological sample from the patient prior to, or earlier in, the therapeutic treatment. Or the sample may be evalated for comparison of protein.
• the present invention provides a method of monitoring the efficacy of a therapeutic treatment of lung cancer, the method comprising the steps of: (i) providing a biological sample from a patient undergoing the therapeutic treatment; and (ii) determining the level of a lung cancer-associated antibody in the biological sample by contacting the biological sample with a polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1A-16, wherein the polypeptide specifically binds to the lung cancer-associated antibody, thereby monitoring the efficacy ofthe therapy.
• the method further comprises the step of: (iii) comparing the level ofthe lung cancer-associated antibody to a level ofthe lung cancer-associated antibody in a biological sample from the patient prior to, or earlier in, the therapeutic treatment.
• the present invention provides a method of monitoring the efficacy of a therapeutic treatment of lung cancer, the method comprising the steps of: (i) providing a biological sample from a patient undergoing the therapeutic treatment; and (ii) determining the level of a lung cancer-associated polypeptide in the biological sample by contacting the biological sample with an antibody, wherein the antibody specifically binds to a polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1 A-16, thereby monitoring the efficacy ofthe therapy.
• the method further comprises the step of: (iii) comparing the level ofthe lung cancer-associated polypeptide to a level ofthe lung cancer-associated polypeptide in a biological sample from the patient prior to, or earlier in, the therapeutic treatment.
• the present invention provides an isolated nucleic acid molecule consisting of a polynucleotide sequence as shown in Tables 1A-16.
• an expression vector or cell comprises the isolated nucleic acid.
• the present invention provides an isolated polypeptide which is encoded by a nucleic acid molecule having polynucleotide sequence as shown in Tables 1 A-16.
• the present invention provides an antibody that specifically binds to an isolated polypeptide which is encoded by a nucleic acid molecule having polynucleotide sequence as shown in Tables 1 A-16.
• the antibody is conjugated to an effector component, e.g., a fluorescent label, a radioisotope or a cytotoxic chemical.
• the antibody is an antibody fragment.
• the antibody is humanized.
• the present invention provides a method of detecting lung cancer in a a patient, the method comprising contacting a biological sample from the patient with an antibody or protein as described herein.
• the present invention provides a method of detecting antibodies specific to a lung cancer gene in a patient, the method comprising contacting a biological sample from the patient with a polypeptide encoded by a nucleic acid comprises a sequence from Tables 1A-16.
• the present invention provides a method for identifying a compound that modulates a lung cancer-associated polypeptide, the method comprising the steps of: (i) contacting the compound with a lung cancer-associated polypeptide, the polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1 A-16; and (ii) determining the functional effect ofthe compound upon the polypeptide.
• the functional effect is a physical effect, an enzymatic effect, or a chemical effect.
• the polypeptide is expressed in a eukaryotic host cell or cell membrane.
• the polypeptide is recombinant.
• the functional effect is determined by measuring ligand binding to the polypeptide.
• the present invention provides a method of inhibiting proliferation or another critical process of a lung cancer-associated cell to treat lung cancer in a patient, the method comprising the step of administering to the subject a therapeutically effective amount of a compound identified as described herein.
• the compound is an antibody.
• the present invention provides a drug screening assay comprising the steps of: (i) administering a test compound to a mammal having lung cancer or a cell isolated therefrom; (ii) comparing the level of gene expression of a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1 A- 16 in a treated cell or mammal with the level of gene expression ofthe polynucleotide in a control cell or mammal, wherein a test compound that modulates the level of expression of the polynucleotide is a candidate for the treatment of lung cancer.
• control is a mammal with lung cancer or a cell therefrom that has not been treated with the test compound. In another embodiment, the control is a normal cell or mammal, or a non-malignant lung disease.
• the present invention provides a method for treating a mammal having lung cancer comprising administering a compound identified by the assay described herein.
• the present invention provides a pharmaceutical composition for treating a mammal having lung cancer, the composition comprising a compound identified by the assay described herein and a physiologically acceptable excipient.
• the present invention provides novel methods for diagnosis and treatment of lung disease or cancer, as well as methods for screening for compositions which modulate lung cancer.
• Treatment, monitoring, detection or modulation of lung disease or cancer includes treatment, monitoring, detection, or modulation of lung disease in those patients who have lung disease (whether malignant or non-malignant, e.g., emphysema, bronchitis, or fibrosis) as well as patients with lung cancers in which gene expression from a gene in Tables 1 A- 16 is increased or decreased, indicating that the subject is more likely to have disease.
• these targets are identified primarily from lung cancer samples, these same targets are likely to be similarly found in analyses of other medical conditions.
• lung cancer small cell lung carcinoma (oat cell carcinoma), non-small cell carcinomas (e.g., squamous cell carcinoma, adenocarcinoma, large cell lung carcinoma, carcinoid, granulomatous), fibrosis (idiopathic pulmonary fibrosis (IPF), hypersensitivity pneumonitis (HP), interstitial pneumonitis, nonspecific idiopathic pneumonitis (NSIP)), chronic obstructive pulmonary disease (COPD, e.g., emphysema, chronic bronchitis), asthma, bronchiectasis, and esophageal cancer.
• lung cancer small cell lung carcinoma
• non-small cell carcinomas e.g., squamous cell carcinoma, adenocarcinoma, large cell lung carcinoma, carcinoid, granulomatous
• fibrosis idiopathic pulmonary fibrosis (IPF)
• HP hypersensitivity pneumonitis
• NIP nonspecific
• the treatment may be of lung cancer or related condition itself, or treatment of metastasis.
• identification of markers selectively expressed on these cancers allows for use of that expression in diagnostic, prognostic, or therapeutic methods.
• the invention defines various compositions, e.g., nucleic acids, polypeptides, antibodies, and small molecule agonists/antagonists, which will be useful to selectively identify those markers.
• therapeutic methods may take the form of protein therapeutics which use the marker expression for selective localization or modulation of function (for those markers which have a causative disease effect), for vaccines, identification of binding partners, or antagonism, e.g., using antisense or RNAi.
• the markers may be useful for molecular characterization of subsets of lung diseases, which subsets may actually require very different treatments.
• the markers may also be important in related diseases to the specific cancers, e.g., which affect similar tissues in non-malignant diseases, or have similar mechanisms of induction/maintenance. Metastatic processes or characteristics may also be targeted. Diagnostic and prognostic uses are made available, e.g., to subset related but distinct diseases, or to determine treatment strategy.
• the detection methods may be based upon nucleic acid, e.g., PCR or hybridization techniques, or protein, e.g., ELISA, imaging, IHC, etc.
• the diagnosis may be qualitative or quantitative, and may detect increases or decreases in expression levels.
• Tables 1A-16 provide unigene cluster identification numbers for the nucleotide sequence of genes that exhibit increased or decreased expression in lung cancer samples. The tables also provide an exemplar accession number that provides a nucleotide sequence that is part ofthe unigene cluster.
• genes marked as "target 1" or “target 2" are particularly useful as therapeutic targets.
• Genes marked as "target 3” are particularly useful as diagnostic markers.
• Genes marked as "chron” are upregulated in chronically diseased lung (e.g., emphysema, bronchitis, fibrosis) relative to lung tumors and normal tissue.
• the ratio for the "chron" category was determined using the 70th percentile of chronically diseases lung samples divided by the 90th percentile of normal lung samples.
• the ratio for the targets was determined using the 70th percentile of lung tumor samples divided by the 90th percentile of normal lung samples.
• lung cancer protein or "lung cancer polynucleotide” or “lung cancer- associated transcript” refers to nucleic acid and polypeptide polymorphic variants, alleles, mutants, and interspecies homologs that: (1) have a nucleotide sequence that has greater than about 60% nucleotide sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or greater nucleotide sequence identity, preferably over a region of over a region of at least about 25, 50, 100, 200, 500, 1000, or more nucleotides, to a nucleotide sequence of or associated with a unigene cluster of Tables 1A-16; (2) bind to antibodies, e.g., polyclonal antibodies, raised against an immunogen comprising an amino acid sequence encoded by a nucleotide sequence of or associated with a unigene cluster of Tables 1A-16
• a polynucleotide or polypeptide sequence is typically from a mammal including, but not limited to, primate, e.g., human; rodent, e.g., rat, mouse, hamster; cow, pig, horse, sheep, or other mammal.
• a "lung cancer polypeptide” and a “lung cancer polynucleotide,” include both naturally occurring or recombinant forms.
• a "full length" lung cancer protein or nucleic acid refers to a lung cancer polypeptide or polynucleotide sequence, or a variant thereof, that contains the elements normally contained in one or more naturally occurring, wild type lung cancer polynucleotide or polypeptide sequences.
• Biological sample as used herein is a sample of biological tissue or fluid that contains nucleic acids or polypeptides, e.g., of a lung cancer protein, polynucleotide, or transcript. Such samples include, but are not limited to, tissue isolated from primates, e.g., humans, or rodents, e.g., mice, and rats. Biological samples may also include sections of tissues such as biopsy and autopsy samples, frozen sections taken for histologic purposes, archival materials, blood, plasma, serum, sputum, stool, tears, mucus, hair, skin, etc.
• Biological samples also include explants and primary and/or transformed cell cultures derived from patient tissues.
• a biological sample is typically obtained from a eukaryotic organism, most preferably a mammal such as a primate, e.g., chimpanzee or human; cow; dog; cat; a rodent, e.g., guinea pig, rat, mouse; rabbit; or other mammal; or a bird; reptile; fish. Livestock and domestic animals are of interest.
• Providing a biological sample means to obtain a biological sample for use in methods described in this invention. Most often, this will be done by removing a sample of cells from an animal, but can also be accomplished by using previously isolated cells (e.g., isolated by another person, at another time, and/or for another purpose), or by performing the methods ofthe invention in vivo. Archival tissues or materials, having treatment or outcome history, will be particularly useful.
• nucleic acids or polypeptide sequences refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (e.g., about 60% identity, preferably 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using, e.g., a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI web site http://www.ncbi.nlm.nih.gov/BLAST/ or the like).
• sequences are then said to be “substantially identical.”
• This definition also refers to, or may be applied to, the complement of a test sequence.
• the definition also includes sequences that have deletions and/or insertions, substitutions, and naturally occurring, e.g., polymorphic or allelic variants, and man-made variants.
• the preferred algorithms can account for gaps and the like.
• identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids or nucleotides in length.
• For sequence comparison typically one sequence acts as a reference sequence, to which test sequences are compared.
• test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Preferably, default program parameters can be used, or alternative parameters can be designated.
• sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
• a “comparison window”, as used herein, includes reference to a segment of contiguous positions selected from the group consisting typically of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
• Methods of alignment of sequences for comparison are well-known in the art.
• Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2:482, by the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity method of Pearson and Lipman (1988) Proc.
• BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins ofthe invention.
• Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/).
• This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive- valued threshold score T when aligned with a word ofthe same length in a database sequence.
• T is referred to as the neighborhood word score threshold (Altschul, et al., supra).
• a scoring matrix is used to calculate the cumulative score. Extension ofthe word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
• the BLAST algorithm parameters W, T, and X determine the sensitivity and speed ofthe alignment.
• the BLAST algorithm also performs a statistical analysis ofthe similarity between two sequences (see, e.g., Karlin and Altschul (1993) Proc. NatT. Acad. Sci. USA 90:5873- 5787).
• P(N) the smallest sum probability
• a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison ofthe test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.
• Log values may be negative large numbers, e.g., 5, 10, 20, 30, 40, 40, 70, 90, 110, 150, 170, etc.
• nucleic acid sequences are substantially identical.
• a polypeptide is typically substantially identical to a second polypeptide, e.g., where the two peptides differ only by conservative substitutions.
• Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions.
• Yet another indication that two nucleic acid sequences are substantially identical is that the same primers can be used to amplify the sequences.
• a "host cell” is a naturally occurring cell or a transformed cell that contains an expression vector and supports the replication or expression ofthe expression vector.
• Host cells may be cultured cells, explants, cells in vivo, and the like.
• Host cells may be prokaryotic cells such as E. coli, or eukaryotic cells such as yeast, insect, amphibian, or mammalian cells such as CHO, HeLa, and the like (see, e.g., the American Type Culture Collection catalog or web site, www.atcc.org).
• isolated refers to material that is substantially or essentially free from components that normally accompany it as found in its native state. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein or nucleic acid that is the predominant species present in a preparation is substantially purified. In particular, an isolated nucleic acid is separated from some open reading frames that naturally flank the gene and encode proteins other than protein encoded by the gene.
• purified in some embodiments denotes that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel.
• nucleic acid or protein is at least about 85% pure, more preferably at least 95% pure, and most preferably at least 99% pure.
• “Purify” or “purification” in other embodiments means removing at least one contaminant or component from the composition to be purified. In this sense, purification does not require that the purified compound be homogeneous, e.g., 100% pure.
• polypeptide peptide
• protein protein
• amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers, those containing modified residues, and non-naturally occurring amino acid polymer.
• amino acid refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function similarly to the naturally occurring amino acids.
• Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, ⁇ - carboxyglutamate, and O-phosphoserine.
• Amino acid analogs refer to compounds that have the same basic chemical structure as a naturally occurring amino acid, e.g., an ⁇ carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium.
• Such analogs may have modified R groups (e.g., norleucine) or modified peptide backbones, but retain some basic chemical structure as a naturally occurring amino acid.
• Amino acid mimetics refer to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that function similarly to another amino acid. Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
• Constantly modified variants applies to both amino acid and nucleic acid sequences.
• conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical or associated, e.g., naturally contiguous, sequences.
• the codons GCA, GCC, GCG, and GCU each encode the amino acid alanine.
• nucleic acid variations are "silent variations," which are one species of conservatively modified variations.
• Every nucleic acid sequence herein which encodes a polypeptide also describes silent variations ofthe nucleic acid.
• each codon in a nucleic acid except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan
• TGG which is ordinarily the only codon for tryptophan
• amino acid sequences one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles ofthe invention.
• Typical conservative substitutions include for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins (1984)). Macromolecular structures such as polypeptide structures can be described in terms of various levels of organization.
• Primary structure refers to the amino acid sequence of a particular peptide.
• Secondary structure refers to locally ordered, three dimensional structures within a polypeptide. These structures are commonly known as domains. Domains are portions of a polypeptide that often form a compact unit ofthe polypeptide and are typically 25 to approximately 500 amino acids long. Typical domains are made up of sections of lesser organization such as stretches of ⁇ -sheet and ⁇ -helices.
• Tumoriary structure refers to the complete three dimensional structure of a polypeptide monomer.
• Quaternary structure refers to the three dimensional structure formed, usually by the noncovalent association of independent tertiary units. Anisotropic terms are also known as energy terms.
• Nucleic acid or “oligonucleotide” or “polynucleotide” or grammatical equivalents used herein means at least two nucleotides covalently linked together. Oligonucleotides are typically from about 5, 6, 7, 8, 9, 10, 12, 15, 25, 30, 40, 50 or more nucleotides in length, up to about 100 nucleotides in length.
• Nucleic acids and polynucleotides are a polymers of any length, including longer lengths, e.g., 200, 300, 500, 1000, 2000, 3000, 5000, 7000, 10,000, etc.
• a nucleic acid ofthe present invention will generally contain phosphodiester bonds, although in some cases, nucleic acid analogs are included that may have at least one different linkage, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or O- methylphophoroamidite linkages (see Eckstein (1992) Oligonucleotides and Analogues: A Practical Approach Oxford University Press); and peptide nucleic acid backbones and linkages.
• nucleic acids include those with positive backbones; non-ionic backbones, and non-ribose backbones, including those described in U.S. Patent Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, in Sanghui and Cook, eds. Carbohydrate Modifications in Antisense Research. ASC Symposium Series 580. Nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids.
• Modifications ofthe ribose-phosphate backbone may be done for a variety of reasons, e.g., to increase the stability and half-life of such molecules in physiological environments or as probes on a biochip.
• Mixtures of naturally occurring nucleic acids and analogs can be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made.
• PNA peptide nucleic acids
• These backbones are substantially non-ionic under neutral conditions, in contrast to the highly charged phosphodiester backbone of naturally occurring nucleic acids. This results in two advantages.
• the PNA backbone exhibits improved hybridization kinetics. PNAs have larger changes in the melting temperature (T m ) for mismatched versus perfectly matched basepairs. DNA and RNA typically exhibit a 2-4° C drop in T m for an internal mismatch. With the non-ionic PNA backbone, the drop is closer to 7-9° C.
• T m melting temperature
• hybridization ofthe bases attached to these backbones is relatively insensitive to salt concentration.
• PNAs are not degraded by cellular enzymes, and thus can be more stable.
• the nucleic acids may be single stranded or double stranded, as specified, or contain portions of both double stranded or single stranded sequence.
• the depiction of a single strand also defines the sequence ofthe complementary strand; thus the sequences described herein also provide the complement ofthe sequence.
• the nucleic acid may be DNA, both genomic and cDNA, RNA, or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases, including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine, isoguanine, etc.
• Transcript typically refers to a naturally occurring RNA, e.g., a pre-mRNA, hnRNA, or mRNA.
• nucleoside includes nucleotides and nucleoside and nucleotide analogs, and modified nucleosides such as amino modified nucleosides.
• nucleoside includes non- naturally occurring analog structures. Thus, e.g., the individual units of a peptide nucleic acid, each containing a base, are referred to herein as a nucleoside.
• a “label” or a “detectable moiety” is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, physiological, chemical, or other physical means.
• useful labels include 32 P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins or other entities which can be made detectable, e.g., by incorporating a radiolabel into the peptide or used to detect antibodies specifically reactive with the peptide.
• the labels may be incorporated into the cancer nucleic acids, proteins, and antibodies. Many methods known in the art for conjugating the antibody to the label may be employed, including those methods described by Hunter, et al.
• effector or “effector moiety” or “effector component” is a molecule that is bound (or linked, or conjugated), either covalently, through a linker or a chemical bond, or noncovalently, through ionic, van der Waals, electrostatic, or hydrogen bonds, to an antibody.
• the "effector” can be a variety of molecules including, e.g., detection moieties including radioactive compounds, fluorescent compounds, an enzyme or substrate, tags such as epitope tags, a toxin; activatable moieties, a chemotherapeutic agent; a lipase; an antibiotic; or a radioisotope emitting "hard” e.g., beta radiation.
• a "labeled nucleic acid probe or oligonucleotide” is one that is bound, either covalently, through a linker or a chemical bond, or noncovalently, through ionic, van der Waals, electrostatic, or hydrogen bonds to a label such that the presence ofthe probe may be detected by detecting the presence ofthe label bound to the probe.
• method using high affinity interactions may achieve the same results where one of a pair of binding partners binds to the other, e.g., biotin, streptavidin.
• nucleic acid probe or oligonucleotide is a nucleic acid capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, e.g., through hydrogen bond formation.
• a probe may include natural (i.e., A, G, C, or T) or modified bases (7-deazaguanosine, inosine, etc.).
• the bases in a probe may be joined by a linkage other than a phosphodiester bond, preferably one that does not functionally interfere with hybridization.
• probes may be peptide nucleic acids in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages. Probes may bind target sequences lacking complete complementarity with the probe sequence depending upon the stringency ofthe hybridization conditions.
• the probes are preferably directly labeled, e.g., with isotopes, chromophores, lumiphores, chromogens, or indirectly labeled, e.g., with biotin to which a streptavidin complex may later bind.
• By assaying for the presence or absence ofthe probe one can detect the presence or absence ofthe select sequence or subsequence. Diagnosis or prognosis may be based at the genomic level, or at the level of RNA or protein expression.
• recombinant when used with reference, e.g., to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified.
• recombinant cells express genes that are not found within the native (non-recombinant) form ofthe cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all.
• nucleic acid By the term “recombinant nucleic acid” herein is meant nucleic acid, originally formed in vitro, in general, by the manipulation of nucleic acid, e.g., using polymerases and endonucleases, in a form not normally found in nature. In this manner, operably linkage of different sequences is achieved.
• an isolated nucleic acid, in a linear form, or an expression vector formed in vitro by ligating DNA molecules that are not normally joined are both considered recombinant for the purposes of this invention.
• a recombinant nucleic acid is made and reinfroduced into a host cell or organism, it will replicate non-recombinantly, i.e., using the in vivo cellular machinery ofthe host cell rather than in vitro manipulations; however, such nucleic acids, once produced recombinanfiy, although subsequently replicated non-recombinantly, are still considered recombinant for the purposes ofthe invention.
• a "recombinant protein” is a protein made using recombinant techniques, i.e., through the expression of a recombinant nucleic acid as depicted above.
• heterologous when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not normally found in the same relationship to each other in nature.
• the nucleic acid is typically recombinanfiy produced, having two or more sequences, e.g., from unrelated genes arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source.
• a heterologous protein will often refer to two or more subsequences that are not found in the same relationship to each other in nature (e.g., a fusion protein).
• a “promoter” is typically an array of nucleic acid control sequences that direct transcription of a nucleic acid.
• a promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element.
• a promoter also optionally includes distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription.
• a “constitutive” promoter is a promoter that is active under most environmental and developmental conditions.
• An “inducible” promoter is a promoter that is active under environmental or developmental regulation.
• operably linked refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, or array of transcription factor binding sites) and a second nucleic acid sequence, e.g., wherein the expression confrol sequence directs transcription ofthe nucleic acid corresponding to the second sequence.
• a nucleic acid expression control sequence such as a promoter, or array of transcription factor binding sites
• an "expression vector” is a nucleic acid construct, generated recombinanfiy or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a host cell.
• the expression vector can be part of a plasmid, virus, or nucleic acid fragment.
• the expression vector includes a nucleic acid to be transcribed in operable linkage to a promoter.
• sequenceselectively (or specifically) hybridizes to refers to the binding, duplexing, or hybridizing of a molecule selectively to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA).
• stringent hybridization conditions refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acids, but to essentially no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures.
• T m thermal melting point
• Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is typically at least two times background, preferably 10 times background hybridization.
• Exemplary stringent hybridization conditions are often: 50% formamide, 5x SSC, and 1% SDS, incubating at 42° C, or, 5x SSC, 1% SDS, incubating at 65° C, with wash in 0.2x SSC, and 0.1%o SDS at 65° C.
• a temperature of about 36° C is typical for low stringency amplification, although annealing temperatures may vary between about 32° C and 48° C depending on primer length.
• a temperature of about 62° C is typical, although high stringency annealing temperatures can range from about 50° C to about 65° C, depending on the primer length and specificity.
• Typical cycle conditions for both high and low stringency amplifications include a denaturation phase of 90° C - 95° C for 0.5 - 2 min., an annealing phase lasting 0.5 - 2 min., and an extension phase of about 72° C for 1 - 2 min. Protocols and guidelines for low and high stringency amplification reactions are provided, e.g., in Innis, et al.(1990) PCR Protocols. A Guide to Methods and Applications.
• Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions.
• Exemplary "moderately stringent hybridization conditions" include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C, and a wash in IX SSC at 45° C. A positive hybridization is at least twice background. Alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency.
• ligand binding activity includes ligand binding activity; cell viability, cell growth on soft agar; anchorage dependence; contact inhibition and density limitation of growth; cellular proliferation; cellular transformation; growth factor or serum dependence; tumor specific marker levels; invasiveness into Matrigel; tumor growth and metastasis in vivo; mRNA and protein expression in cells undergoing metastasis, and other characteristics of lung cancer cells.
• “Functional effects” include in vitro, in vivo, and ex vivo activities.
• determining the functional effect is meant assaying for a compound that increases or decreases a parameter that is indirectly or directly under the influence of a lung cancer protein sequence, e.g., physiological, functional, enzymatic, physical, or chemical effects.
• Such functional effects can be measured by many means known to those skilled in the art, e.g., changes in spectroscopic characteristics (e.g., fluorescence, absorbance, refractive index), hydrodynamic (e.g., shape), chromatographic, or solubility properties for the protein, measuring inducible markers or transcriptional activation ofthe lung cancer protein; measuring binding activity or binding assays, e.g., binding to antibodies or other ligands, and measuring cellular proliferation.
• spectroscopic characteristics e.g., fluorescence, absorbance, refractive index
• hydrodynamic e.g., shape
• chromatographic, or solubility properties for the protein
• solubility properties for the protein measuring inducible markers or transcriptional activation ofthe lung cancer protein
• binding activity or binding assays e.g., binding to antibodies or other ligands, and measuring cellular proliferation.
• Determination ofthe functional effect of a compound on lung cancer can also be performed using lung cancer assays known to those of skill in the art such as an in vitro assays, e.g., cell growth on soft agar; anchorage dependence; contact inhibition and density limitation of growth; cellular proliferation; cellular transformation; growth factor or serum dependence; tumor specific marker levels; invasiveness into Matrigel; tumor growth and metastasis in vivo; mRNA and protein expression in cells undergoing metastasis, and other characteristics of lung cancer cells.
• lung cancer assays known to those of skill in the art such as an in vitro assays, e.g., cell growth on soft agar; anchorage dependence; contact inhibition and density limitation of growth; cellular proliferation; cellular transformation; growth factor or serum dependence; tumor specific marker levels; invasiveness into Matrigel; tumor growth and metastasis in vivo; mRNA and protein expression in cells undergoing metastasis, and other characteristics of lung cancer cells.
• the functional effects can be evaluated by many means known to those skilled in the art, e.g., microscopy for quantitative or qualitative measures of alterations in morphological features, measurement of changes in RNA or protein levels for lung cancer-associated sequences, measurement of RNA stability, identification of downstream or reporter gene expression (CAT, luciferase, ⁇ -gal, GFP, and the like), e.g., via chemiluminescence, fluorescence, colorimetric reactions, antibody binding, inducible markers, and ligand binding assays.
• CAT reporter gene expression
• Inhibitors are used to refer to activating, inhibitory, or modulating molecules or compounds identified using in vitro and in vivo assays of lung cancer polynucleotide and polypeptide sequences.
• Inhibitors are compounds that, e.g., bind to, partially or totally block activity, decrease, prevent, delay activation, inactivate, desensitize, or down regulate the activity or expression of lung cancer proteins, e.g., antagonists.
• Antisense or inhibitory nucleic acids may seem to inhibit expression and subsequent function ofthe protein.
• Activators are compounds that increase, open, activate, facilitate, enhance activation, sensitize, agonize, or up regulate lung cancer protein activity.
• Inhibitors, activators, or modulators also include genetically modified versions of lung cancer proteins, e.g., versions with altered activity, as well as naturally occurring and synthetic ligands, antagonists, agonists, antibodies, small chemical molecules and the like.
• Such assays for inhibitors and activators include, e.g., expressing the lung cancer protein in vitro, in cells, or cell membranes, applying putative modulator compounds, and then determining the functional effects on activity, as described above.
• Activators and inhibitors of lung cancer can also be identified by incubating lung cancer cells with the test compound and determining increases or decreases in the expression of 1 or more lung cancer proteins, e.g., 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50 or more lung cancer proteins, such as lung cancer proteins encoded by the sequences set out in Tables 1A-16.
• 1 or more lung cancer proteins e.g., 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50 or more lung cancer proteins, such as lung cancer proteins encoded by the sequences set out in Tables 1A-16.
• Samples or assays comprising lung cancer proteins that are treated with a potential activator, inhibitor, or modulator are compared to control samples without the inhibitor, activator, or modulator to examine the extent of inhibition.
• Control samples (untreated with inhibitors) are assigned a relative protein activity value of 100%. Inhibition of a polypeptide is achieved when the activity value relative to the control is about 80%, preferably 50%, more preferably 25-0%.
• Activation of a lung cancer polypeptide is achieved when the activity value relative to the control (untreated with activators) is 110%, more preferably 150%, more preferably 200-500% (i.e., two to five fold higher relative to the control), more preferably 1000-3000% higher.
• change in cell growth refers to any change in cell growth and proliferation characteristics in vitro or in vivo, such as cell viability, formation of foci, anchorage independence, semi-solid or soft agar growth, changes in contact inhibition and density limitation of growth, loss of growth factor or serum requirements, changes in cell morphology, gaining or losing immortalization, gaining or losing tumor specific markers, ability to form or suppress tumors when injected into suitable animal hosts, and/or immortalization ofthe cell. See, e.g., Freshney (1994) Culture of Animal Cells a Manual of Basic Technique pp. 231-241 (3 rd ed.).
• Tumor cell refers to precancerous, cancerous, and normal cells in a tumor.
• Cancer cells “transformed” cells, or “transformation” in tissue culture, refers to spontaneous or induced phenotypic changes that do not necessarily involve the uptake of new genetic material. Although fransformation can arise from infection with a transforming virus and incorporation of new genomic DNA, or uptake of exogenous DNA, it can also arise spontaneously or following exposure to a carcinogen, thereby mutating an endogenous gene.
• Antibody refers to a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen.
• the recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda.
• Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD, and IgE, respectively.
• the antigen-binding region of an antibody or its functional equivalent will be most critical in specificity and affinity of binding. See Paul, Fundamental Immunology.
• An exemplary immunoglobulin (antibody) structural unit comprises a tetramer.
• Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light” (about 25 kD) and one "heavy” chain (about 50-70 kD).
• the N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition.
• the terms variable light chain (V ) and variable heavy chain (V H ) refer to these light and heavy chains respectively.
• Antibodies exist, e.g., as intact immunoglobulins or as a number of well-characterized fragments produced by digestion with various peptidases.
• pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)' 2) a dimer of Fab which itself is a light chain joined to V H -C H 1 by a disulfide bond.
• the F(ab)' 2 may be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab)' 2 dimer into an Fab' monomer.
• the Fab' monomer is essentially Fab with part ofthe hinge region (see Paul (ed.
• antibody fragments are defined in terms ofthe digestion of an intact antibody, one of skill will appreciate that such fragments may be synthesized de novo either chemically or by using recombinant DNA methodology.
• the term antibody also includes antibody fragments either produced by the modification of whole antibodies, or those synthesized de novo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g., McCafferty, et al. (1990) Nature 348:552- 554).
• Patent 4,946,778 can be adapted to produce antibodies to polypeptides of this invention.
• transgenic mice, or other organisms such as other mammals may be used to express humanized antibodies.
• phage display technology can be used to identify antibodies and heteromeric Fab fragments that specifically bind to selected antigens (see, e.g., McCafferty, et al. (1990) Nature 348:552-554; Marks, et al. (1992) Biotechnology 10:779-783).
• a “chimeric antibody” is an antibody molecule in which, e.g, (a) the constant region, or a portion thereof, is altered, replaced, or exchanged so that the antigen binding site (variable region) is linked to a constant region of a different or altered class, effector function, and/or species, or an entirely different molecule which confers new properties to the chimeric antibody, e.g., an enzyme, toxin, hormone, growth factor, drug, etc.; or (b) the variable region, or a portion thereof, is altered, replaced, or exchanged with a variable region having a different or altered antigen specificity.
• the expression levels of genes are determined in different patient samples for which diagnosis information is desired, to provide expression profiles.
• An expression profile of a particular sample is essentially a "fingerprint" ofthe state ofthe sample; while two states may have any particular gene similarly expressed, the evaluation of a number of genes simultaneously allows the generation of a gene expression profile that is characteristic ofthe state ofthe cell. That is, normal tissue may be distinguished from cancerous or metastatic cancerous tissue, or metastatic cancerous tissue can be compared with tissue from surviving cancer patients.
• expression profiles of tissue in known different lung cancer states information regarding which genes are important (including both up- and down-regulation of genes) in each of these states is obtained.
• Molecular profiling may distinguish subtypes of a currently collective disease designation, e.g., different forms of lung cancer (chronic disease, adenocarcinoma, etc.)
• sequences that are differentially expressed in lung cancer versus non-lung cancer tissue allows the use of this information in a number of ways. For example, a particular freatment regime may be evaluated: does a chemotherapeutic drug act to down- regulate lung cancer, and thus tumor growth or recurrence, in a particular patient.
• a freatment step may induce other markers which may be used as targets to destroy tumor cells.
• diagnosis and freatment outcomes may be done or confirmed by comparing patient samples with the known expression profiles. Malignant diseasemay be compared to non-malignant conditions. Metastatic tissue can also be analyzed to determine the stage of lung cancer in the tissue, or origin of primary tumor, e.g., metastasis from a remote primary site.
• these gene expression profiles allow screening of drug candidates with an eye to mimicking or altering a particular expression profile; e.g., screening can be done for drugs that suppress the lung cancer expression profile. This may be done by making biochips comprising sets ofthe important lung cancer genes, which can then be used in these screens.
• PCR methods may be applied with selected primer pairs, and analysis may be of RNA or of genomic sequences. These methods can also be done on the protein basis; that is, protein expression levels ofthe lung cancer proteins can be evaluated for diagnostic purposes or to screen candidate agents.
• the lung cancer nucleic acid sequences can be administered for gene therapy purposes, including the adminisfration of antisense nucleic acids, or the lung cancer proteins (including antibodies and other modulators thereof) administered as therapeutic drugs or as protein or DNA vaccines.
• lung cancer sequences include those that are up-regulated (i.e., expressed at a higher level) in lung cancer, as well as those that are down-regulated (i.e., expressed at a lower level).
• the lung cancer sequences are from humans; however, as will be appreciated by those in the art, lung cancer sequences from other organisms may be useful in animal models of disease and drug evaluation; thus, other lung cancer sequences are provided, from vertebrates, including mammals, including rodents (rats, mice, hamsters, guinea pigs, etc.), primates, farm animals (including sheep, goats, pigs, cows, horses, etc.) and pets (dogs, cats, etc.). Lung cancer sequences from other organisms may be obtained using the techniques outlined below.
• Lung cancer sequences can include both nucleic acid and amino acid sequences.
• lung cancer nucleic acid sequences are useful in a variety of applications, including diagnostic applications, which will detect naturally occurring nucleic acids, as well as screening applications; e.g., biochips comprising nucleic acid probes or PCR microtiter plates with selected probes to the lung cancer sequences can be generated.
• a lung cancer sequence can be initially identified by substantial nucleic acid and/or amino acid sequence homology to the lung cancer sequences outlined herein. Such homology can be based upon the overall nucleic acid or amino acid sequence, and is generally determined as outlined below, e.g., using homology programs or hybridization conditions.
• the lung cancer screen typically includes comparing genes identified in different tissues, e.g., normal and cancerous tissues, cancer and non-malignant conditions, non-malignant conditions and normal tissues, or tumor tissue samples from patients who have metastatic disease vs. non metastatic tissue.
• Other suitable tissue comparisons include comparing lung cancer samples with metastatic cancer samples from other cancers, such as, breast, other gastrointestinal cancers, prostate, ovarian, etc.
• Samples of, non metastatic disease tissue and tissue undergoing metastasis are applied to biochips comprising nucleic acid probes. The samples are first microdissected, if applicable, and treated as is known in the art for the preparation of mRNA. Suitable biochips are commercially available, e.g., from Affymetrix, Santa Clara, CA. Gene expression profiles as described herein are generated and the data analyzed.
• the genes showing changes in expression as between normal and disease states are compared to genes expressed in other normal tissues, preferably normal lung, but also including, and not limited to colon, heart, brain, liver, breast, kidney, muscle, prostate, small intestine, large intestine, spleen, bone, and/or placenta.
• those genes identified during the lung cancer screen that are expressed in significant amounts in other tissues are removed from the profile, although in some embodiments, this is not necessary (e.g., where organs may be dispensible at a later stage of life). That is, when screening for drugs, it is usually preferable that the target expression be disease specific, to minimize possible side effects on other organs.
• lung cancer sequences are those that are up-regulated in lung cancer; that is, the expression of these genes is higher in cancerous tissue than in normal lung or other tissue.
• Up-regulation means, when the ratio is presented as a number greater than one, that the ratio is greater than one, preferably 1.5 or greater, more preferably 2.0 or greater.
• Another embodiment is directed to sequences up-regulated in non- malignant conditions relative to normal.
• Unigene cluster identification numbers and accession numbers herein are for the GenBank sequence database and the sequences ofthe accession numbers are hereby expressly incorporated by reference.
• GenBank is known in the art, see, e.g., Benson, DA, et al (1998) Nucleic Acids Research 26:1-7 and http://www.ncbi.nlm.nih.gov/. Sequences are also available in other databases, e.g., European Molecular Biology Laboratory (EMBL) and DNA Database of Japan (DDBJ). Another embodiment is directed to sequences up-regulated in non-malignant conditions relative to normal. In some situations, the sequences may be derived from assembly of available sequences or be predicted from genomic DNA using exon prediction algorithms, such as FGENESH (Salamov and Solovyev (2000) Genome Res. 10:516-522). In other situations, sequences have been derived from cloning and sequencing of isolated nucleic acids.
• lung cancer sequences are those that are downregulated in the lung cancer; that is, the expression of these genes is lower in cancerous tissue or normal lung or other tissue.
• Down-regulation as used herein means, when the ratio is presented as a number greater than one, that the ratio is greater than one, preferably 1.5 or greater, more preferably 2.0 or greater, or, when the ratio is presented as a number less than one, that the ratio is less than one, preferably 0.5 or less, more preferably 0.25 or less.
• the ability to identify genes that are over or under expressed in lung cancer can additionally provide high-resolution, high-sensitivity datasets which can be used in the areas of diagnostics, therapeutics, drug development, pharmacogenetics, protein structure, biosensor development, and other related areas.
• the expression profiles can be used in diagnostic or prognostic evaluation of patients with lung cancer.
• subcellular toxicological information can be generated to better direct drug stracture and activity correlation (see Anderson (1998) Pharmaceutical Proteomics: Targets. Mechanism, and Function, paper presented at the IBC Proteomics conference, Coronado, CA (June 11-12, 1998)).
• the present invention provides a database that includes at least one set of assay data.
• the data contained in the database is acquired, e.g., using array analysis either singly or in a library format.
• the database can be in a form in which data can be maintained and transmitted, but is preferably an electronic database.
• the electronic database ofthe invention can be maintained on any electronic device allowing for the storage of and access to the database, such as a personal computer, but is preferably distributed on a wide area network, such as the World Wide Web.
• compositions and methods for identifying and/or quantitating the relative and/or absolute abundance of a variety of molecular and macromolecular species from a biological sample representing lung cancer i.e., the identification of lung cancer-associated sequences described herein, provide an abundance of information, which can be correlated with pathological conditions, predisposition to disease, drag testing, therapeutic monitoring, gene- disease causal linkages, identification of correlates of immunity and physiological status, among others.
• data generated from the assays ofthe invention is suited for manual review and analysis, in a preferred embodiment, data processing using high-speed computers is utilized.
• U.S. Patents 6,023,659 and 5,966,712 disclose a relational database system for storing biomolecular sequence information in a manner that allows sequences to be catalogued and searched according to one or more protein function hierarchies.
• U.S. Patent 5,953,727 discloses a relational database having sequence records containing information in a format that allows a collection of partial-length DNA sequences to be catalogued and searched according to association with one or more sequencing projects for obtaining full-length sequences from the collection of partial length sequences.
• Patent 5,706,498 discloses a gene database retrieval system for making a retrieval of a gene sequence similar to a sequence data item in a gene database based on the degree of similarity between a key sequence and a target sequence.
• U.S. Patent 5,538,897 discloses a method using mass spectroscopy fragmentation patterns of peptides to identify amino acid sequences in computer databases by comparison of predicted mass specfra with experimentally-derived mass spectra using a closeness-of-fit measure.
• U.S. Patent 5,926,818 discloses a multi- dimensional database comprising a functionality for multi-dimensional data analysis described as on-line analytical processing (OLAP), which entails the consolidation of projected and actual data according to more than one consolidation path or dimension.
• OLAP on-line analytical processing
• Patent 5,295,261 reports a hybrid database stracture in which the fields of each database record are divided into two classes, navigational and informational data, with navigational fields stored in a hierarchical topological map which can be viewed as a tree stracture or as the merger of two or more such tree structures.
• the present invention provides a computer database comprising a computer and software for storing in computer-retrievable form assay data records cross-tabulated, e.g., with data specifying the source ofthe target-containing sample from which each sequence specificity record was obtained.
• At least one ofthe sources of target-containing sample is from a control tissue sample known to be free of pathological disorders.
• at least one ofthe sources is a known pathological tissue specimen, e.g., a neoplastic lesion or another tissue specimen to be analyzed for lung cancer.
• the assay records cross-tabulate one or more ofthe following parameters for each target species in a sample: (1) a unique identification code, which can include, e.g., a target molecular structure and/or characteristic separation coordinate (e.g., electrophoretic coordinates); (2) sample source; and (3) absolute and/or relative quantity ofthe target species present in the sample.
• the invention also provides for the storage and retrieval of a collection of target data in a computer data storage apparatus, which can include magnetic disks, optical disks, magneto-optical disks, DRAM, SRAM, SGRAM, SDRAM, RDRAM, DDR RAM, magnetic bubble memory devices, and other data storage devices, including CPU registers and on-CPU data storage arrays.
• the target data records are stored as a bit pattern in an array of magnetic domains on a magnetizable medium or as an array of charge states or transistor gate states, such as an array of cells in a DRAM device (e.g., each cell comprised of a transistor and a charge storage area, which may be on the transistor).
• the invention provides such storage devices, and computer systems built therewith, comprising a bit pattern encoding a protein expression fingerprint record comprising unique identifiers for at least 10 target data records cross-tabulated with target source.
• the invention preferably provides a method for identifying related peptide or nucleic acid sequences, comprising performing a computerized comparison between a peptide or nucleic acid sequence assay record stored in or retrieved from a computer storage device or database and at least one other sequence.
• the comparison can include a sequence analysis or comparison algorithm or computer program embodiment thereof (e.g., FASTA, TFASTA, GAP, BESTFIT) and/or the comparison may be ofthe relative amount of a peptide or nucleic acid sequence in a pool of sequences determined from a polypeptide or nucleic acid sample of a specimen.
• the invention also preferably provides a magnetic disk, such as an IBM-compatible (DOS, Windows, Windows95/98/2000, Windows NT, OS/2) or other format (e.g., Linux, SunOS, Solaris, ATX, SCO Unix, VMS, MV, Macintosh, etc.) floppy diskette or hard (fixed, Winchester) disk drive, comprising a bit pattern encoding data from an assay ofthe invention in a file format suitable for retrieval and processing in a computerized sequence analysis, comparison, or relative quantitation method.
• a magnetic disk such as an IBM-compatible (DOS, Windows, Windows95/98/2000, Windows NT, OS/2) or other format (e.g., Linux, SunOS, Solaris, ATX, SCO Unix, VMS, MV, Macintosh, etc.) floppy diskette or hard (fixed, Winchester) disk drive, comprising a bit pattern encoding data from an assay ofthe invention in a file format suitable for retrieval and processing
• the invention also provides a network, comprising a plurality of computing devices linked via a data link, such as an Ethernet cable (coax or lOBaseT), telephone line, ISDN line, wireless network, optical fiber, or other suitable signal transmission medium, whereby at least one network device (e.g., computer, disk array, etc.) comprises a pattern of magnetic domains (e.g., magnetic disk) and/or charge domains (e.g., an array of DRAM cells) composing a bit pattern encoding data acquired from an assay ofthe invention.
• a network device e.g., computer, disk array, etc.
• a pattern of magnetic domains e.g., magnetic disk
• charge domains e.g., an array of DRAM cells
• the invention also provides a method for transmitting assay data that includes generating an electronic signal on an electronic communications device, such as a modem, ISDN terminal adapter, DSL, cable modem, ATM switch, or the like, wherein the signal includes (in native or encrypted format) a bit pattern encoding data from an assay or a database comprising a plurality of assay results obtained by the method ofthe invention.
• the invention provides a computer system for comparing a query target to a database containing an array of data structures, such as an assay result obtained by the method ofthe invention, and ranking database targets based on the degree of identity and gap weight to the target data.
• a central processor is preferably initialized to load and execute the computer program for alignment and/or comparison ofthe assay results. Data for a query target is entered into the central processor via an I/O device. Execution of the computer program results in the central processor retrieving the assay data from the data file, which comprises a binary description of an assay result.
• the target data or record and the computer program can be transferred to secondary memory, which is typically random access memory (e.g., DRAM, SRAM, SGRAM, or SDRAM).
• Targets are ranked according to the degree of correspondence between a selected assay characteristic (e.g., binding to a selected affinity moiety) and the same characteristic of the query target and results are output via an I/O device.
• a central processor can be a conventional computer (e.g., Intel Pentium, PowerPC, Alpha, PA-8000, SPARC, MIPS 4400, MIPS 10000, VAX, etc.);
• a program can be a commercial or public domain molecular biology software package (e.g., UWGCG Sequence Analysis Software, Darwin);
• a data file can be an optical or magnetic disk, a data server, a memory device (e.g., DRAM, SRAM, SGRAM, SDRAM, EPROM, bubble memory, flash memory, etc.);
• an I/O device can be a terminal comprising a video display and a keyboard, a modem, an ISDN terminal adapter, an Ethernet port, a punched card reader, a magnetic strip reader, or other suitable I/O device.
• the invention also preferably provides the use of a computer system, such as that described above, which comprises: (1) a computer; (2) a stored bit pattern encoding a collection of peptide sequence specificity records obtained by the methods ofthe invention, which may be stored in the computer; (3) a comparison target, such as a query target; and (4) a program for alignment and comparison, typically with rank-ordering of comparison results on the basis of computed similarity values.
• a computer system such as that described above, which comprises: (1) a computer; (2) a stored bit pattern encoding a collection of peptide sequence specificity records obtained by the methods ofthe invention, which may be stored in the computer; (3) a comparison target, such as a query target; and (4) a program for alignment and comparison, typically with rank-ordering of comparison results on the basis of computed similarity values.
• Lung cancer proteins ofthe present invention may be classified as secreted proteins, transmembrane proteins or intracellular proteins.
• the lung cancer protein is an intracellular protein.
• Intracellular proteins may be found in the cytoplasm and/or in the nucleus. Intracellular proteins are involved in all aspects of cellular function and replication (including, e.g., signaling pathways); aberrant expression of such proteins often results in unregulated or disregulated cellular processes (see, e.g., Alberts (ed. 1994) Molecular Biology ofthe Cell (3d ed.).
• intracellular proteins have enzymatic activity such as protein kinase activity, protein phosphatase activity, protease activity, nucleotide cyclase activity, polymerase activity and the like.
• Intracellular proteins also serve as docking proteins that are involved in organizing complexes of proteins, or targeting proteins to various subcellular localizations, and are involved in maintaining the structural integrity of organelles.
• Src-homology-2 (SH2) domains bind tyrosine-phosphorylated targets in a sequence dependent manner.
• PTB domains which are distinct from SH2 domains, also bind tyrosine phosphorylated targets.
• SH3 domains bind to proline-rich targets.
• PH domains, tetratricopeptide repeats and WD domains have been shown to mediate protein-protein interactions.
• Pfam protein families
• Pfam protein families
• the lung cancer sequences are fransmembrane proteins.
• Transmembrane proteins are molecules that span a phosphohpid bilayer of a cell. They may have an intracellular domain, an extracellular domain, or both. The intracellular domains of such proteins may have a number of functions including those already described for intracellular proteins. For example, the intracellular domain may have enzymatic activity and/or may serve as a binding site for additional proteins. Frequently the intracellular domain of transmembrane proteins serves both roles. For example certain receptor tyrosine kinases have both protein kinase activity and SH2 domains. In addition, autophosphorylation of tyrosines on the receptor molecule itself, creates binding sites for additional SH2 domain containing proteins. Transmembrane proteins may contain from one to many transmembrane domains.
• receptor tyrosine kinases For example, receptor tyrosine kinases, certain cytokine receptors, receptor guanylyl cyclases and receptor serine/threonine protein kinases contain a single transmembrane domain.
• various other proteins including channels, pumps, and adenylyl cyclases contain numerous transmembrane domains.
• Many important cell surface receptors such as G protein coupled receptors (GPCRs) are classified as "seven fransmembrane domain" proteins, as they contain 7 membrane spanning regions. Characteristics of transmembrane domains include approximately 17 consecutive hydrophobic amino acids that may be followed by charged amino acids.
• the localization and number of fransmembrane domains within the protein may be predicted (see, e.g., PSORT web site http://psort.nibb.ac.jp/).
• extracellular domains of transmembrane proteins are diverse; however, conserved motifs are found repeatedly among various extracellular domains. conserveed structure and/or functions have been ascribed to different exfracellular motifs. Many extracellular domains are involved in binding to other molecules. In one aspect, extracellular domains are found on receptors. Factors that bind the receptor domain include circulating ligands, which may be peptides, proteins, or small molecules such as adenosine and the like. For example, growth factors such as EGF, FGF, and PDGF are circulating growth factors that bind to their cognate receptors to initiate a variety of cellular responses. Other factors include cytokines, mitogenic factors, hormones, neurotrophic factors and the like.
• Extracellular domains also bind to cell-associated molecules. In this respect, they may mediate cell-cell interactions.
• Cell-associated ligands can be tethered to the cell, e.g., via a glycosylphosphatidylinositol (GPI) anchor, or may themselves be transmembrane proteins.
• Extracellular domains may also associate with the extracellular matrix and contribute to the maintenance ofthe cell structure.
• Lung cancer proteins that are fransmembrane are particularly preferred in the present invention as they are readily accessible targets for exfracellular immunotherapeutics, as are described herein.
• transmembrane proteins can be also useful in imaging modalities.
• Antibodies may be used to label such readily accessible proteins in situ or in histological analysis.
• antibodies can also label intracellular proteins, in which case analytical samples are typically permeablized to provide access to intracellular proteins.
• some membrane proteins can be processed to release a soluble protein, or to expose a residual fragment. Released soluble proteins may be useful diagnostic markers, processed residual protein fragments may be useful lung markers of disease.
• transmembrane protein can be made soluble by removing fransmembrane sequences, e.g., through recombinant methods.
• transmembrane proteins that have been made soluble can be made to be secreted through recombinant means by adding an appropriate signal sequence.
• the lung cancer proteins are secreted proteins; the secretion of which can be either constitutive or regulated. These proteins may have a signal peptide or signal sequence that targets the molecule to the secretory pathway. Secreted proteins are involved in numerous physiological events; e.g., if circulating, they often serve to transmit signals to various other cell types.
• the secreted protein may function in an autocrine manner (acting on the cell that secreted the factor), a paracrine manner (acting on cells in close proximity to the cell that secreted the factor), an endocrine manner (acting on cells at a distance, e.g., secretion into the blood stream), or exocrine (secretion, e.g., through a duct or to adjacent epithelial surface as sweat glands, sebaceous glands, pancreatic ducts, lacrimal glands, mammary glands, sax producing glands ofthe ear, etc.).
• secreted molecules often find use in modulating or altering numerous aspects of physiology.
• Lung cancer proteins that are secreted proteins are particularly preferred in the present invention as they serve as good targets for diagnostic markers, e.g., for blood, plasma, serum, or stool tests.
• diagnostic markers e.g., for blood, plasma, serum, or stool tests.
• Those which are enzymes may be antibody or small molecule targets.
• Others may be useful as vaccine targets, e.g., via CTL mechanisms.
• lung cancer sequence is initially identified by substantial nucleic acid and/or amino acid sequence homology or linkage to the lung cancer sequences outlined herein. Such homology can be based upon the overall nucleic acid or amino acid sequence, and is generally determined as outlined below, using either homology programs or hybridization conditions. Typically, linked sequences on a mRNA are found on the same molecule.
• the lung cancer nucleic acid sequences ofthe invention e.g., the sequences in Tables
• Genes 1A-16 can be fragments of larger genes, i.e., they are nucleic acid segments. "Genes" in this context includes coding regions, non-coding regions, and mixtures of coding and non-coding regions. Accordingly, as will be appreciated by those in the art, using the sequences provided herein, extended sequences, in either direction, ofthe lung cancer genes can be obtained, using techniques well known in the art for cloning either longer sequences or the full length sequences; see Ausubel, et al, supra.
• a lung cancer nucleic acid Once a lung cancer nucleic acid is identified, it can be cloned and, if necessary, its constituent parts recombined to form the entire lung cancer nucleic acid coding regions or the entire mRNA sequence.
• the recombinant lung cancer nucleic acid Once isolated from its natural source, e.g., contained within a plasmid or other vector or excised therefrom as a linear nucleic acid segment, the recombinant lung cancer nucleic acid can be further-used as a probe to identify and isolate other lung cancer nucleic acids, e.g., extended coding regions. It can also be used as a "precursor" nucleic acid to make modified or variant lung cancer nucleic acids and proteins.
• the lung cancer nucleic acids ofthe present invention are used in several ways.
• nucleic acid probes to the lung cancer nucleic acids are made and attached to biochips to be used in screening and diagnostic methods, as outlined below, or for administration, e.g., for gene therapy, RNAi, vaccine, and/or antisense applications.
• the lung cancer nucleic acids that include coding regions of lung cancer proteins can be put into expression vectors for the expression of lung cancer proteins, again for screening purposes or for administration to a patient.
• nucleic acid probes to lung cancer nucleic acids are made.
• the nucleic acid probes attached to the biochip are designed to be substantially complementary to the lung cancer nucleic acids, i.e., the target sequence (either the target sequence ofthe sample or to other probe sequences, e.g., in sandwich assays), such that hybridization of the target sequence and the probes of the present invention occurs.
• the target sequence either the target sequence ofthe sample or to other probe sequences, e.g., in sandwich assays
• this complementarity need not be perfect; there may be any number of base pair mismatches which will interfere with hybridization between the target sequence and the single stranded nucleic acids ofthe present invention.
• the sequence is not a complementary target sequence.
• substantially complementary herein is meant that the probes are sufficiently complementary to the target sequences to hybridize under appropriate reaction conditions, particularly high stringency conditions, as outlined herein.
• a nucleic acid probe is generally single stranded but can be partially single and partially double stranded.
• the sfrandedness ofthe probe is dictated by the structure, composition, and properties ofthe target sequence.
• the nucleic acid probes range from about 8 to about 100 bases long, with from about 10 to about 80 bases being preferred, and from about 30 to about 50 bases being particularly preferred. That is, generally complements of ORFs or whole genes are not used.
• nucleic acids of lengths up to hundreds of bases can be used.
• more than one probe per sequence is used, with either overlapping probes or probes to different sections ofthe target being used. That is, two, three, four or more probes, with three being preferred, are used to build in a redundancy for a particular target.
• the probes can be overlapping (i.e., have some sequence in common), or separate.
• PCR primers may be used to amplify signal for higher sensitivity.
• nucleic acids can be attached or immobilized to a solid support in a wide variety of ways.
• immobilized and grammatical equivalents herein is meant the association or binding between the nucleic acid probe and the solid support is sufficient to be stable under the conditions of binding, washing, analysis, and removal as outlined below.
• the binding can typically be covalent or non-covalent.
• non- covalent binding and grammatical equivalents herein is typically meant one or more of electrostatic, hydrophilic, and hydrophobic interactions. Included in non-covalent binding is the covalent attachment of a molecule, such as, streptavidin to the support and the non- covalent binding ofthe biotinylated probe to the streptavidin.
• covalent binding and grammatical equivalents herein is meant that the two moieties, the solid support and the probe, are attached by at least one bond, including sigma bonds, pi bonds and coordination bonds. Covalent bonds can be formed directly between the probe and the solid support or can be formed by a cross linker or by inclusion of a specific reactive group on either the solid support or the probe or both molecules. Immobilization may also involve a combination of covalent and non-covalent interactions.
• the probes are attached to a biochip in a wide variety of ways, as will be appreciated by those in the art.
• the nucleic acids can either be synthesized first, with subsequent attachment to the biochip, or can be directly synthesized on the biochip.
• the biochip comprises a suitable solid substrate.
• substrate or “solid support” or other grammatical equivalents herein is meant a material that can be modified for the attachment or association ofthe nucleic acid probes and is amenable to at least one detection method. Often the substrate may contain discrete individual sites appropriate for ndivitual partitioning and identification.
• the number of possible substrates are very large, and include, but are not limited to, glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, Teflon, etc.), polysaccharides, nylon or nitrocellulose, resins, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses, plastics, etc.
• the substrates allow optical detection and do not appreciably fluoresce.
• a preferred substrate is described in US application entitled Reusable Low Fluorescent Plastic Biochip, U.S. Application Serial No. 09/270,214, filed March 15, 1999, herein inco ⁇ orated by reference in its entirety.
• the substrate is planar, although as will be appreciated by those in the art, other configurations of substrates may be used as well.
• the probes may be placed on the inside surface of a tube, for flow-through sample analysis to minimize sample volume.
• the substrate may be flexible, such as a flexible foam, including closed cell foams made of particular plastics.
• the surface ofthe biochip and the probe may be derivatized with chemical functional groups for subsequent attachment ofthe two.
• the biochip is derivatized with a chemical functional group including, but not limited to, amino groups, carboxy groups, oxo groups and thiol groups, with amino groups being particularly preferred.
• the probes can be attached using functional groups on the probes.
• nucleic acids containing amino groups can be attached to surfaces comprising amino groups, e.g., using linkers as are known in the art; e.g., homo-or hetero-bifunctional linkers as are well known (see 1994 Pierce Chemical Company catalog, technical section on cross-linkers, pages 155-200).
• additional linkers such as alkyl groups (including substituted and heteroalkyl groups) may be used.
• oligonucleotides are synthesized, and then attached to the surface ofthe solid support. Either the 5' or 3' terminus may be attached to the solid support, or attachment may be via linkage to an internal nucleoside.
• the immobilization to the solid support may be very strong, yet non-covalent.
• biotinylated oligonucleotides can be made, which bind to surfaces covalently coated with streptavidin, resulting in attachment.
• the oligonucleotides may be synthesized on the surface, as is known in the art.
• photoactivation techniques utilizing photopolymerization compounds and techniques are used.
• the nucleic acids can be synthesized in situ, using known photolithographic techniques, such as those described in WO 95/25116;
• amplification-based assays are performed to measure the expression level of lung cancer-associated sequences. These assays are typically performed in conjunction with reverse transcription.
• a lung cancer-associated nucleic acid sequence acts as a template in an amplification reaction (e.g., Polymerase Chain Reaction, or PCR).
• an amplification reaction e.g., Polymerase Chain Reaction, or PCR.
• the amount of amplification product will be proportional to the amount of template in the original sample. Comparison to appropriate controls provides a measure ofthe amount of lung cancer-associated RNA.
• Methods of quantitative amplification are well known to those of skill in the art. Detailed protocols for quantitative PCR are provided, e.g., in Innis, et al. (1990) PCR Protocols. A Guide to Methods and Applications.
• a TaqMan based assay is used to measure expression.
• TaqMan based assays use a fluorogenic oligonucleotide probe that contains a 5' fluorescent dye and a 3' quenching agent. The probe hybridizes to a PCR product, but cannot itself be extended due to a blocking agent at the 3 ' end.
• the 5' nuclease activity ofthe polymerase e.g., AmpliTaq
• This cleavage separates the 5' fluorescent dye and the 3' quenching agent, thereby resulting in an increase in fluorescence as a function of amplification (see, e.g., literature provided by Perkin-Elmer, e.g., www2.perkin-elmer.com).
• ligase chain reaction (LCR) (see Wu and Wallace (1989) Genomics 4:560, Landegren, et al. (1988) Science 241:1077, and Barringer, et al. (1990) Gene 89:117), transcription amplification (Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173), self-sustained sequence replication (Guatelli, et al. (1990) Proc. Nat. Acad. Sci. USA 87:1874), dot PCR, and linker adapter PCR, etc.
• LCR ligase chain reaction
• lung cancer nucleic acids e.g., encoding lung cancer proteins
• lung cancer nucleic acids are used to make a variety of expression vectors to express lung cancer proteins which can then be used in screening assays, as described below.
• Expression vectors and recombinant DNA technology are well known to those of skill in the art (see, e.g., Ausubel, supra, and Fernandez and Hoeffler (eds 1999) Gene Expression Systems and are used to express proteins.
• the expression vectors may be either self-replicating exfrachromosomal vectors or vectors which integrate into a host genome.
• these expression vectors include transcriptional and translational regulatory nucleic acid operably linked to the nucleic acid encoding the lung cancer protein.
• control sequences refers to DNA sequences used for the expression of an operably linked coding sequence in a particular host organism. Control sequences that are suitable for prokaryotes, e.g., include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers. Nucleic acid is "operably linked” when it is placed into a functional relationship with another nucleic acid sequence.
• DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion ofthe polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription ofthe sequence; or a ribosome bmding site is operably linked to a coding sequence if it is positioned so as to facilitate franslation.
• "operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is typically accomplished by ligation at convenient restriction sites.
• Transcriptional and translational regulatory nucleic acid will generally be appropriate to the host cell used to express the lung cancer protein. Numerous types of appropriate expression vectors, and suitable regulatory sequences are known in the art for a variety of host cells.
• transcriptional and translational regulatory sequences may include, but are not limited to, promoter sequences, ribosomal binding sites, franscriptional start and stop sequences, translational start and stop sequences, and enhancer or activator sequences.
• the regulatory sequences include a promoter and transcriptional start and stop sequences.
• Promoter sequences may be either constitutive or inducible promoters.
• the promoters may be either naturally occurring promoters or hybrid promoters.
• Hybrid promoters which combine elements of more than one promoter, are also known in the art, and are useful in the present invention.
• an expression vector may comprise additional elements.
• the expression vector may have two replication systems, thus allowing it to be maintained in two organisms, e.g., in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification.
• the expression vector often contains at least one sequence homologous to the host cell genome, and preferably two homologous sequences which flank the expression construct.
• the integrating vector may be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. Constructs for integrating vectors are well known in the art (e.g., Fernandez and Hoeffler, supra).
• the expression vector contains a selectable marker gene to allow the selection of transformed host cells.
• Selection genes are well known in the art and will vary with the host cell used.
• the lung cancer proteins ofthe present invention are usually produced by culturing a host cell transformed with an expression vector containing nucleic acid encoding a lung cancer protein, under the appropriate conditions to induce or cause expression ofthe lung cancer protein.
• Conditions appropriate for lung cancer protein expression will vary with the choice ofthe expression vector and the host cell, and will be easily ascertained by one skilled in the art through routine experimentation or optimization.
• the use of constitutive promoters in the expression vector will require optimizing the growth and proliferation ofthe host cell, while the use of an inducible promoter requires the appropriate growth conditions for induction.
• the timing ofthe harvest is important.
• the baculoviral systems used in insect cell expression are lytic viruses, and thus harvest time selection can be crucial for product yield.
• Appropriate host cells include yeast, bacteria, archaebacteria, fungi, and insect and animal cells, including mammalian cells. Of particular interest are Saccharomyces cerevisiae and other yeasts, E. coli, Bacillus subtilis, Sf9 cells, C129 cells, 293 cells, Neurospora, BHK, CHO, COS, HeLa cells, HUV ⁇ C (human umbilical vein endothelial cells), THP1 cells (a macrophage cell line) and various other human cells and cell lines.
• the lung cancer proteins are expressed in mammalian cells.
• Mammalian expression systems are also known in the art, and include retroviral and adenoviral systems.
• mammalian promoters are the promoters from mammalian viral genes, since the viral genes are often highly expressed and have a broad host range. Examples include the SV40 early promoter, mouse mammary tumor virus LTR promoter, adenovirus major late promoter, he ⁇ es simplex virus promoter, and the CMV promoter (see, e.g., Fernandez and Hoeffler, supra).
• transcription termination and polyadenylation sequences recognized by mammalian cells are regulatory regions located 3 ' to the translation stop codon and thus, together with the promoter elements, flank the coding sequence.
• transcription terminator and polyadenylation signals include those derived form SV40.
• the methods of introducing exogenous nucleic acid into mammalian hosts, as well as other hosts, is well known in the art, and will vary with the host cell used. Techniques include dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, viral infection, encapsulation ofthe 5 polynucleotide(s) in liposomes, and direct microinjection ofthe DNA into nuclei.
• lung cancer proteins are expressed in bacterial systems. Promoters from bacteriophage may also be used and are known in the art. In addition, synthetic promoters and hybrid promoters are also useful; e.g., the tac promoter is a hybrid of the t ⁇ and lac promoter sequences. Furthermore, a bacterial promoter can include naturally
• the expression vector may also include a signal peptide sequence that provides for secretion ofthe lung cancer protein in bacteria. The protein is either secreted into the growth media (gram-positive bacteria) or into the
• the bacterial expression vector may also include a selectable marker gene to allow for the selection of bacterial strains that have been transformed. Suitable selection genes include genes which render the bacteria resistant to drags such as ampicillin, chloramphenicol, erythromycin, kanamycin, neomycin and tetracycline. Selectable markers
• .0 also include biosynthetic genes, such as those in the histidine, tryptophan and leucine biosynthetic pathways. These components are assembled into expression vectors.
• Expression vectors for bacteria are well known in the art, and include vectors for Bacillus subtilis, E. coli, Streptococcus cremoris, and Streptococcus lividans, among others (e.g., Fernandez and Hoeffler, supra). The bacterial expression vectors are transformed into bacterial host cells
• lung cancer proteins are produced in insect cells.
• Expression vectors for the fransformation of insect cells and in particular, baculoviras-based expression vectors, are well known in the art.
• lung cancer protein is produced in yeast cells.
• yeast expression systems are well known in the art, and include expression vectors for Saccharomyces cerevisiae, Candida albicans and C. maltosa, Hansenula polymorpha, Kluyveromyces fragilis and K. lactis, Pichia guillerimondii, and P. pastoris, Schizosaccharomyces pombe, and Yarrowia lipolytica.
• the lung cancer protein may also be made as a fusion protein, using techniques well known in the art. Thus, e.g., for the creation of monoclonal antibodies, if the desired epitope is small, the lung cancer protein may be fused to a carrier protein to form an immunogen. Alternatively, the lung cancer protein may be made as a fusion protein to increase expression for affinity purification pu ⁇ oses, or for other reasons. For example, when the lung cancer protein is a lung cancer peptide, the nucleic acid encoding the peptide may be linked to other nucleic acid for expression purposes. In a preferred embodiment, the lung cancer protein is purified or isolated after expression. Lung cancer proteins may be isolated or purified in a variety of appropriate ways.
• Standard purification methods include electrophoretic, molecular, immunological and chromatographic techniques, including ion exchange, hydrophobic, affinity, and reverse- phase HPLC chromatography, and chromatofocusing.
• the lung cancer protein may be purified using a standard anti-lung cancer protein antibody column. Ulfrafiltration and diafilfration techniques, in conjunction with protein concenfration, are also useful.
• suitable purification techniques see Scopes (1982) Protein Purification. The degree of purification necessary will vary depending on the use ofthe lung cancer protein. In some instances no purification will be necessary.
• the lung cancer proteins and nucleic acids are useful in a number of applications. They may be used as immunoselection reagents, as vaccine reagents, as screening agents, therapeutic entities, for production of antibodies, as transcription or translation inhibitors, etc.
• the lung cancer proteins are derivative or variant lung cancer proteins as compared to the wild-type sequence. That is, as outlined more fully below, the derivative lung cancer peptide will often contain at least one amino acid substitution, deletion or insertion, with amino acid substitutions being particularly preferred. The amino acid substitution, insertion or deletion may occur at a particular residue within the lung cancer peptide.
• amino acid sequence variants typically fall into one or more of three classes: substitutional, insertional or deletional variants. These variants ordinarily are prepared by site specific mutagenesis of nucleotides in the DNA encoding the lung cancer protein, using cassette or PCR mutagenesis or other techniques, to produce DNA encoding the variant, and thereafter expressing the DNA in recombinant cell culture as outlined above. However, variant lung cancer protein fragments having up to about 100-150 residues may be prepared by in vitro synthesis. Amino acid sequence variants are characterized by the predetermined nature ofthe variation, a feature that sets them apart from naturally occurring allelic or interspecies variation ofthe lung cancer protein amino acid sequence. The variants typically exhibit a similar qualitative biological activity as the naturally occurring analogue, although variants can also be selected which have modified characteristics as will be more fully outlined below.
• the mutation per se need not be predetermined.
• random mutagenesis may be conducted at the target codon or region and the expressed lung cancer variants screened for the optimal combination of desired activity.
• Techniques exist for making substitution mutations at predetermined sites in DNA having a known sequence e.g., Ml 3 primer mutagenesis and PCR mutagenesis. Screening of mutants is often done using assays of lung cancer protein activities.
• Amino acid substitutions are typically of single residues; insertions usually will be on the order of from about 1 to 20 amino acids, although considerably larger insertions may be occasionally tolerated.
• Deletions generally range from about 1 to about 20 residues, although in some cases deletions may be much larger.
• substitutions, deletions, insertions or any combination thereof may be used to arrive at a final derivative. Generally these changes are done on a few amino acids to minimize the alteration ofthe molecule. Larger changes may be tolerated in certain circumstances.
• substitutions are generally made in accordance with the amino acid substitution chart provided in the definition section. Variants typically exhibit essentially the same qualitative biological activity and will elicit the same immune response as a naturally-occurring analog, although variants also are selected to modify the characteristics of lung cancer proteins as needed. Alternatively, the variant may be designed or reorganized such that a biological activity ofthe lung cancer protein is altered. For example, glycosylation sites may be added, altered, or removed.
• Covalent modifications of lung cancer polypeptides are included within the scope of this invention.
• One type of covalent modification includes reacting targeted amino acid residues of a lung cancer polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N-or C-terminal residues of a lung cancer polypeptide.
• Derivatization with bifunctional agents is useful, for instance, for crosslinking lung cancer polypeptides to a water-insoluble support matrix or surface for use in a method for purifying anti-lung cancer polypeptide antibodies or screening assays, as is more fully described below.
• crosslinking agents include, e.g., l,l-bis(diazoacetyl)-2- phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, e.g., esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3'- dithiobis(succinimidylpropionate), bifunctional maleimides such as bis-N-maleimido-1,8- octane and agents such as methyl-3-((p-azidophenyl)dithio)propioimidate.
• l,l-bis(diazoacetyl)-2- phenylethane glutaraldehyde
• N-hydroxysuccinimide esters e.g., esters with 4-azidosalicylic acid
• homobifunctional imidoesters including disuccinimidyl esters such
• Another type of covalent modification ofthe lung cancer polypeptide encompassed by this invention is an altered native glycosylation pattern ofthe polypeptide.
• "Altering the native glycosylation pattern” is intended herein to mean adding to or deleting one or more carbohydrate moieties of a native sequence lung cancer polypeptide.
• Glycosylation patterns can be altered in many ways. For example the use of different cell types to express lung cancer-associated sequences can result in different glycosylation patterns.
• Addition of glycosylation sites to lung cancer polypeptides may also be accomplished by altering the amino acid sequence thereof.
• the alteration may be made, e.g., by the addition of, or substitution by, one or more serine or threonine residues to the native sequence lung cancer polypeptide (for O-linked glycosylation sites).
• the lung cancer amino acid sequence may optionally be altered through changes at the DNA level, particularly by mutating the DNA encoding the lung cancer polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids.
• Another means of increasing the number of carbohydrate moieties on the lung cancer polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide.
• Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of endo-and exo-glycosidases as described by Thotakura, et al. (1987) Meth. Enzymol.. 138:350.
• Another type of covalent modification of lung cancer comprises linking the lung cancer polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Patent Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192, or 4,179,337.
• nonproteinaceous polymers e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes
• Lung cancer polypeptides ofthe present invention may also be modified in a way to form chimeric molecules comprising a lung cancer polypeptide fused to another, heterologous polypeptide or amino acid sequence.
• a chimeric molecule comprises a fusion of a lung cancer polypeptide with a tag polypeptide which provides an epitope to which an anti-tag antibody can selectively bind.
• the epitope tag is generally placed at the amino-or carboxyl-terminus ofthe lung cancer polypeptide. The presence of such epitope-tagged forms of a lung cancer polypeptide can be detected using an antibody against the tag polypeptide.
• the epitope tag enables the lung cancer polypeptide to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag.
• the chimeric molecule may comprise a fusion of a lung cancer polypeptide with an immunoglobulin or a particular region of an immunoglobulin.
• such a fusion could be to the Fc region of an IgG molecule.
• tag polypeptides and their respective antibodies are well known and examples include poly-histidine (poly-his) or poly-histidine-glycine (poly-his-gly) tags; HIS6 and metal chelation tags, the flu HA tag polypeptide and its antibody 12CA5 (Field, et al. (1988) Mol. Cell. Biol. 8:2159-2165); the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto (Evan, et al. (1985) Molecular and Cellular Biology 5:3610-3616); and the He ⁇ es Simplex virus glycoprotein D (gD) tag and its antibody (Paborsky, et al.
• tag polypeptides include the Flag-peptide (Hopp, et al. (1988) BioTechnology 6:1204-1210); the KT3 epitope peptide (Martin, et al. (1992) Science 255:192-194); tubulin epitope peptide (Skinner, et al. (1991) J. Biol. Chem. 266:15163- 15166); and the T7 gene 10 protein peptide tag (Lutz-Freyermuth, et al. (1990) Proc. Nat'l Acad. Sci. USA 87:6393-6397).
• probe or degenerate polymerase chain reaction (PCR) primer sequences may be used to find other related lung cancer proteins from primates or other organisms.
• probe or degenerate polymerase chain reaction (PCR) primer sequences include unique areas ofthe lung cancer nucleic acid sequence.
• preferred PCR primers are from about 15 to about 35 nucleotides in length, with from about 20 to about 30 being preferred, and may contain inosine as needed.
• PCR reaction conditions are well known in the art (e.g., Innis, PCR Protocols, supra).
• the lung cancer protein when a lung cancer protein is to be used to generate antibodies, e.g., for immunotherapy or immunodiagnosis, the lung cancer protein should share at least one epitope or determinant with the full length protein.
• epitope or “determinant” herein is typically meant a portion of a protein which will generate and/or bind an antibody or T-cell receptor in the context of MHC.
• epitope is unique; that is, antibodies generated to a unique epitope show little or no cross-reactivity.
• polyclonal antibodies can be raised in a mammal, e.g., by one or more injections of an immunizing agent and, if desired, an adjuvant.
• an immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections.
• the immunizing agent may include a protein encoded by a nucleic acid of Tables 1 A- 16 or fragment thereof or a fusion protein thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized.
• Immunogenic proteins include, e.g., keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor.
• Adjuvants include, e.g., Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).
• the immunization protocol may be selected by one skilled in the art.
• the antibodies may, alternatively, be monoclonal antibodies.
• Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein (1975) Nature 256:495.
• a hybridoma method a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immumzing agent.
• the lymphocytes may be immunized in vitro.
• the immunizing agent will typically include a polypeptide encoded by a nucleic acid ofthe tables, or fragment thereof, or a fusion protein thereof.
• peripheral blood lymphocytes are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non- human mammalian sources are desired.
• the lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding (1986) Monoclonal Antibodies: Principles and Practice, pp. 59-103 ).
• Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovin, or primate origin. Usually, rat or mouse myeloma cell lines are employed.
• the hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival ofthe unfused, immortalized cells.
• a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival ofthe unfused, immortalized cells.
• the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine ("HAT medium"), which substances prevent the growth of HGPRT-deficient cells.
• the antibodies are bispecific antibodies.
• Bispecific antibodies are typically monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens or that have binding specificities for two epitopes on the same antigen.
• one ofthe binding specificities is for a protein encoded by a nucleic acid ofthe tables or a fragment thereof, the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit, preferably one that is tumor specific.
• teframer-type technology may create multivalent reagents.
• the antibodies to lung cancer protein are capable of reducing or eliminating a biological function of a lung cancer protein, in a naked form or conjugated to an effector moiety. That is, the addition of anti-lung cancer protein antibodies (either polyclonal or preferably monoclonal) to lung cancer tissue (or cells containing lung cancer) may reduce or eliminate the lung cancer. Generally, at least a 25% decrease in activity, growth, size or the like is preferred, with at least about 50% being particularly preferred and about a 95-100%) decrease being especially preferred.
• the antibodies to the lung cancer proteins are humanized antibodies (e.g., Xenerex Biosciences, Medarex, Inc., Abgenix, Inc., Protein Design Labs, Inc.)
• Humanized forms of non-human (e.g., murine) antibodies are chimeric molecules of immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin.
• Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) ofthe recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity.
• CDR complementary determining region
• donor antibody non-human species
• Fv framework residues of a human immunoglobulin are replaced by corresponding non-human residues.
• Humanized antibodies may also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences.
• a humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all ofthe CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework (FR) regions are those of a human immunoglobulin consensus sequence.
• a humanized antibody optimally also will typically comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones, et al. (1986) Nature 321:522-525; Riechmann, et al. (1988) Nature 332:323-329; and Presta (1992) Curr. Op. Struct. Biol. 2:593-596).
• Humanization can be performed following the method of Winter and co-workers (Jones, et al. (1986) Nature 321:522-525; Riechmann, et al. (1988) Nature 332:323-327; Verhoeyen, et al. (1988) Science 239:1534-1536), by substituting rodent CDRs or CDR sequences for corresponding sequences of a human antibody.
• rodent CDRs or CDR sequences for corresponding sequences of a human antibody.
• humanized antibodies are chimeric antibodies (U.S. Patent No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by corresponding sequence from a non-human species.
• Human-like antibodies can also be produced using various techniques known in the art, including phage display libraries (Hoogenboom and Winter (1991) J.
• human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated.
• immunotherapy freatment of lung cancer with an antibody raised against a lung cancer proteins.
• immunotherapy can be passive or active.
• Passive immunotherapy as defined herein is the passive transfer of antibody to a recipient (patient).
• Active immunization is the induction of antibody and/or T-cell responses in a recipient (patient).
• Induction of an immune response is the result of providing the recipient with an antigen to which antibodies are raised.
• the antigen may be provided by injecting a polypeptide against which antibodies are desired to be raised into a recipient, or contacting the recipient with a nucleic acid capable of expressing the antigen and under conditions for expression ofthe antigen, leading to an immune response.
• the lung cancer proteins against which antibodies are raised are secreted proteins as described above.
• antibodies used for freatment may bind and prevent the secreted protein from binding to its receptor, thereby inactivating the secreted lung cancer protein.
• the lung cancer protein to which antibodies are raised is a transmembrane protein.
• antibodies used for treatment may bind the exfracellular domain ofthe lung cancer protein and prevent it from binding to other proteins, such as circulating ligands or cell-associated molecules.
• the antibody may cause down-regulation ofthe transmembrane lung cancer protein.
• the antibody may be a competitive, non-competitive or uncompetitive inhibitor of protein binding to the exfracellular domain ofthe lung cancer protein.
• the antibody may be an antagonist of the lung cancer protein or may prevent activation of a fransmembrane lung cancer protein, or may induce or suppress a particular cellular pathway. In some embodiments, when the antibody prevents the binding of other molecules to the lung cancer protein, the antibody prevents growth ofthe cell.
• the antibody may also be used to target or sensitize the cell to cytotoxic agents, including, but not limited to TNF- ⁇ , TNF- ⁇ , IL-1, LNF- ⁇ , and IL-2, or chemotherapeutic agents including 5FU, vinblastine, actinomycin D, cisplatin, methofrexate, and the like.
• the antibody may belong to a sub-type that activates seram complement when complexed with the transmembrane protein thereby mediating cytotoxicity or antigen-dependent cytotoxicity (ADCC).
• ADCC antigen-dependent cytotoxicity
• lung cancer may be treated by administering to a patient antibodies directed against the transmembrane lung cancer protein.
• Antibody-labeling may activate a co-toxin, localize a toxin payload, or otherwise provide means to locally ablate cells.
• the antibody is conjugated to an effector moiety.
• the effector moiety can be various molecules, including labeling moieties such as radioactive labels or fluorescent labels, or can be a therapeutic moiety.
• the therapeutic moiety is a small molecule that modulates the activity of a lung cancer protein.
• the therapeutic moiety may modulate an activity of molecules associated with or in close proximity to a lung cancer protein.
• the therapeutic moiety may inhibit enzymatic or signaling activity such as protease or coUagenase activity associated with lung cancer.
• the therapeutic moiety can also be a cytotoxic agent.
• targeting the cytotoxic agent to lung cancer tissue or cells results in a reduction in the number of afflicted cells, thereby reducing symptoms associated with lung cancer.
• Cytotoxic agents are numerous and varied and include, but are not limited to, cytotoxic drugs or toxins or active fragments of such toxins. Suitable toxins and their corresponding fragments include diphtheria A chain, exotoxin A chain, ricin A chain, abrin A chain, curcin, crotin, phenomycin, enomycin, saporin, auristatin, and the like. Cytotoxic agents also include radiochemicals made by conjugating radioisotopes to antibodies raised against lung cancer proteins, or binding of a radionuclide to a chelating agent that has been covalently attached to the antibody. Targeting the therapeutic moiety to transmembrane lung cancer proteins not only serves to increase the local concentration of therapeutic moiety in the lung cancer afflicted area, but also serves to reduce deleterious side effects that may be associated with the untargeted therapeutic moiety.
• the lung cancer protein against which the antibodies are raised is an intracellular protein.
• the antibody may be conjugated to a protein or other entity which facilitates entry into the cell.
• the antibody enters the cell by endocytosis.
• a nucleic acid encoding the antibody is administered to the individual or cell.
• an antibody thereto may contain a signal for that target localization, i.e., a nuclear localization signal.
• the lung cancer antibodies ofthe invention specifically bind to lung cancer proteins.
• the antibodies bind to the protein with a K of at least about 0.1 mM, more usually at least about 1 ⁇ M, preferably at least about 0.1 ⁇ M or better, and most preferably, 0.01 ⁇ M or better. Selectivity of binding to the specific target and not to related other sequences is also important.
• the RNA expression levels of genes are determined for different cellular states in the lung cancer phenotype. Expression levels of genes in normal tissue (e.g., not undergoing lung cancer), in lung cancer tissue (and in some cases, for varying severities of lung cancer that relate to prognosis, as outlined below), or in non-malignant disease are evaluated to provide expression profiles.
• a gene expression profile of a particular cell state or point of development is essentially a "finge ⁇ rint" ofthe state ofthe cell. While two states may have a particular gene similarly expressed, the evaluation of a number of genes simultaneously allows the generation of a gene expression profile that is reflective ofthe state ofthe cell.
• a qualitatively regulated gene will exhibit an expression pattern within a state or cell type which is detectable by standard techniques. Some genes will be expressed in one state or cell type, but not in both. Alternatively, the difference in expression may be quantitative, e.g., in that expression is increased or decreased; i.e., gene expression is either upregulated, resulting in an increased amount of transcript, or downregulated, resulting in a decreased amount of transcript.
• the degree to which expression differs need only be large enough to quantify via standard characterization techniques as outlined below, such as by use of Affymetrix GeneChipTM expression arrays, Lockhart (1996) Nature Biotechnology 14: 1675-1680, hereby expressly inco ⁇ orated by reference.
• the change in expression is typically at least about 50%, more preferably at least about 100%, more preferably at least about 150%, more preferably at least about 200%, with from 300 to at least 1000% being especially preferred.
• Evaluation may be at the gene transcript or the protein level.
• the amount of gene expression may be monitored using nucleic acid probes to the RNA or DNA equivalent ofthe gene transcript, and the quantification of gene expression levels, or, alternatively, the final gene product itself (protein) can be monitored, e.g., with antibodies to the lung cancer protein and standard immunoassays (ELISAs, etc.) or other techniques, including mass spectroscopy assays, 2D gel electrophoresis assays, etc.
• Proteins corresponding to lung cancer genes e.g., those identified as being important in a lung cancer or disease phenotype, can be evaluated in a lung cancer diagnostic test.
• gene expression monitoring is performed simultaneously on a number of genes.
• the lung cancer nucleic acid probes may be attached to biochips as outlined herein for the detection and quantification of lung cancer sequences in a particular cell.
• the assays are further described below in the example. PCR techniques can be used to provide greater sensitivity. Multiple protein expression monitoring can be performed as well. Similarly, these assays may be performed on an individual basis as well.
• nucleic acids encoding the lung cancer protein are detected.
• DNA or RNA encoding the lung cancer protem may be detected, of particular interest are methods wherein an mRNA encoding a lung cancer protein is detected.
• Probes to detect mRNA can be a nucleotide/deoxynucleotide probe that is complementary to and hybridizes with the mRNA and includes, but is not limited to, oligonucleotides, cDNA or RNA. Probes also should contain a detectable label, as defined herein.
• the mRNA is detected after immobilizing the nucleic acid to be examined on a solid support such as nylon membranes and hybridizing the probe with the sample.
• RNA probe digoxygenin labeled riboprobe (RNA probe) that is complementary to the mRNA encoding a lung cancer protein is detected by binding the digoxygenin with an anti-digoxygenin secondary antibody and developed with nitro blue tetrazolium and 5-bromo-4-chloro-3-indoyl phosphate.
• various proteins from the three classes of proteins as described herein are used in diagnostic assays.
• the lung cancer proteins, antibodies, nucleic acids, modified proteins and cells containing lung cancer sequences are used in diagnostic assays. This can be performed on an individual gene or corresponding polypeptide level.
• the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes and/or corresponding polypeptides.
• lung cancer proteins find use as markers of lung cancer, e.g., for prognostic or diagnostic pu ⁇ oses. Detection of these proteins in putative lung cancer tissue allows for detection, prognosis, or diagnosis of lung cancer or similar disease, and perhaps for selection of therapeutic strategy.
• antibodies are used to detect lung cancer proteins.
• a preferred method separates proteins from a sample by electrophoresis on a gel (typically a denaturing and reducing protein gel, but may be another type of gel, including isoelectric focusing gels and the like). Following separation of proteins, the lung cancer protein is detected, e.g., by immunoblotting with antibodies raised against the lung cancer protein. Methods of immunoblotting are well known to those of ordinary skill in the art.
• antibodies to the lung cancer protein find use in in situ imaging techniques, e.g., in histology (e.g., Asai (ed. 1993) Methods in Cell Biology: Antibodies in Cell Biology, volume 37.
• cells are contacted with from one to many antibodies to the lung cancer protein(s). Following washing to remove non-specific antibody binding, the presence ofthe antibody or antibodies is detected.
• the antibody is detected by incubating with a secondary antibody that contains a detectable label, e.g., multicolor fluorescence or confocal imaging.
• the primary antibody to the lung cancer protein(s) contains a detectable label, e.g., an enzyme marker that can act on a substrate.
• each one of multiple primary antibodies contains a distinct and detectable label. This method finds particular use in simultaneous screening for a plurality of lung cancer proteins. Many other histological imaging techniques are also provided by the invention.
• the label is detected in a fluorometer which has the ability to detect and distinguish emissions of different wavelengths.
• a fluorescence activated cell sorter FACS
• FACS fluorescence activated cell sorter
• antibodies find use in diagnosing lung cancer from blood, serum, plasma, stool, and other samples. Such samples, therefore, are useful as samples to be probed or tested for the presence of lung cancer proteins.
• Antibodies can be used to detect a lung cancer protein by previously described immunoassay techniques including ELISA, immunoblotting (western blotting), immunoprecipitation, BIACORE technology and the like. Conversely, the presence of antibodies may indicate an immune response against an endogenous lung cancer protein or vaccine.
• in situ hybridization of labeled lung cancer nucleic acid probes to tissue arrays is done.
• arrays of tissue samples, including lung cancer tissue and/or normal tissue are made.
• In situ hybridization (see, e.g., Ausubel, supra) is then performed.
• the skilled artisan can make a diagnosis, a prognosis, or a prediction based on the findings. It is further understood that the genes which indicate the diagnosis may differ from those which indicate the prognosis and molecular profiling ofthe condition ofthe cells may lead to distinctions between responsive or refractory conditions or may be predictive of outcomes.
• the lung cancer proteins, antibodies, nucleic acids, modified proteins and cells containing lung cancer sequences are used in prognosis assays.
• gene expression profiles can be generated that correlate to lung cancer, clinical, pathological, or other information, in terms of long term prognosis. Again, this may be done on either a protein or gene level, with the use of genes being preferred. Single or multiple genes may be useful in various combinations.
• lung cancer probes may be attached to biochips for the detection and quantification of lung cancer sequences in a tissue or patient. The assays proceed as outlined above for diagnosis. PCR method may provide more sensitive and accurate quantification.
• the proteins, nucleic acids, and antibodies as described herein are used in drug screening assays.
• the lung cancer proteins, antibodies, nucleic acids, modified proteins and cells containing lung cancer sequences are used in drug screening assays or by evaluating the effect of drug candidates on a "gene expression profile" or expression profile of polypeptides.
• the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes after freatment with a candidate agent (e.g., Zlokarnik, et al. (1998) Science 279:84-8; Heid (1996) Genome Res. 6:986-94.
• the lung cancer proteins, antibodies, nucleic acids, modified proteins and cells containing the native or modified lung cancer proteins are used in screening assays. That is, the present invention provides novel methods for screening for compositions which modulate the lung cancer phenotype or an identified physiological function of a lung cancer protein. As above, this can be done on an individual gene level or by evaluating the effect of drag candidates on a "gene expression profile".
• the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes after treatment with a candidate agent, see Zlokarnik, supra.
• assays may be performed.
• assays may be ran on an individual gene or protein level. That is, having identified a particular gene with altered regulation in lung cancer, test compounds can be screened for the ability to modulate gene expression or for binding to the lung cancer protein.
• “Modulation” thus includes an increase or a decrease in gene expression. The preferred amount of modulation will depend on the original change ofthe gene expression in normal versus tissue undergoing lung cancer, with changes of at least 10%, preferably 50%, more preferably 100-300%, and in some embodiments 300-1000%) or greater.
• a gene exhibits a 4-fold increase in lung cancer tissue compared to normal tissue, a decrease of about four-fold is often desired; similarly, a 10-fold decrease in lung cancer tissue compared to normal tissue often provides a target value of a 10-fold increase in expression to be induced by the test compound.
• the amount of gene expression may be monitored using nucleic acid probes and the quantification of gene expression levels, or, alternatively, the gene product itself can be monitored, e.g., through the use of antibodies to the lung cancer protein and standard immunoassays. Proteomics and separation techniques may also allow quantification of expression.
• gene or protein expression monitoring of a number of entities i.e., an expression profile
• Such profiles will typically involve a plurality of those entities described herein.
• the lung cancer nucleic acid probes are attached to biochips as outlined herein for the detection and quantification of lung cancer sequences in a particular cell.
• PCR may be used.
• a series e.g., of microtiter plate, may be used with dispensed primers in desired wells. A PCR reaction can then be performed and analyzed for each well.
• Expression monitoring can be performed to identify compounds that modify the expression of one or more lung cancer-associated sequences, e.g., a polynucleotide sequence set out in the tables.
• a test compound is added to the cells prior to analysis.
• screens are also provided to identify agents that modulate lung cancer, modulate lung cancer proteins, bind to a lung cancer protein, or interfere with the binding of a lung cancer protein and an antibody, substrate, or other binding partner.
• test compound or “drag candidate” or “modulator” or grammatical equivalents as used herein describes a molecule, e.g., protein, oligopeptide, small organic molecule, polysaccharide, polynucleotide, etc., to be tested for the capacity to directly or. indirectly alter the lung cancer phenotype or the expression of a lung cancer sequence, e.g., a nucleic acid or protein sequence.
• modulators alter expression profiles of nucleic acids or proteins provided herein.
• the modulator suppresses a lung cancer phenotype, e.g., to a normal or non-malignant tissue finge ⁇ rint.
• a modulator induces a lung cancer phenotype.
• a plurality of assay mixtures are run in parallel with different agent concentrations to obtain a differential response to the various concentrations.
• one of these concentrations serves as a negative control, i.e., at zero concentration or below the level of detection.
• a modulator will neutralize the effect of a lung cancer protein.
• neutralize is meant that activity of a protein and the consequent effect on the cell is inhibited or blocked.
• combinatorial libraries of potential modulators will be screened for an ability to bind to a lung cancer polypeptide or to modulate activity.
• new chemical entities with useful properties are generated by identifying a chemical compound (called a “lead compound”) with some desirable property or activity, e.g., inhibiting activity, creating variants ofthe lead compound, and evaluating the property and activity of those variant compounds.
• a chemical compound called a “lead compound”
• HTS high throughput screening
• high throughput screening methods involve providing a library containing a large number of potential therapeutic compounds (candidate compounds). Such "combinatorial chemical libraries” are then screened in one or more assays to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional "lead compounds” or can themselves be used as potential or actual therapeutics.
• a combinatorial chemical library is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis by combining a number of chemical "building blocks" such as reagents.
• a linear combinatorial chemical library such as a polypeptide (e.g., mutein) library, is formed by combining a set of chemical building blocks called amino acids in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound). Millions of chemical compounds can be synthesized through such combinatorial mixing of chemical building blocks (Gallop, et al. (1994) J. Med. Chem. 37(9):1233-1251). Preparation and screening of combinatorial chemical libraries is well known to those of skill in the art.
• Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Patent No. 5,010,175, Furka (1991) Pept. Prot. Res. 37:487- 493, Houghton, et al. (1991) Nature. 354:84-88), peptoids (PCT Publication No WO 91/19735), encoded peptides (PCT Publication WO 93/20242), random bio-oligomers (PCT Publication WO 92/00091), benzodiazepines (U.S. Pat. No.
• the assays to identify modulators are amenable to high throughput screening. Preferred assays thus detect modulation of lung cancer gene transcription, polypeptide expression, and polypeptide activity.
• High throughput assays for evaluating the presence, absence, quantification, or other properties of particular nucleic acids or protein products are well known to those of skill in the art.
• binding assays and reporter gene assays are similarly well known.
• U.S. Patent No. 5,559,410 discloses high throughput screening methods for proteins
• U.S. Patent No. 5,585,639 discloses high throughput screening methods for nucleic acid binding (i.e., in arrays)
• U.S. Patent Nos. 5,576,220 and 5,541,061 disclose high throughput methods of screening for ligand/antibody binding.
• modulators are proteins, often naturally occurring proteins or fragments of naturally occurring proteins.
• cellular extracts containing proteins, or random or directed digests of proteinaceous cellular extracts may be used.
• libraries of proteins may be made for screening in the methods ofthe invention.
• Particularly preferred in this embodiment are libraries of bacterial, fungal, viral, and mammalian proteins, with the latter being preferred, and human proteins being especially preferred.
• Particularly useful test compound will be directed to the class of proteins to which the target belongs, e.g., substrates for enzymes or ligands and receptors.
• modulators are peptides of from about 5 to about 30 amino acids, with from about 5 to about 20 amino acids being preferred, and from about 7 to about 15 being particularly preferred.
• the peptides may be digests of naturally occurring proteins, random peptides, or "biased” random peptides.
• randomized or grammatical equivalents herein is meant that the nucleic acid or peptide consists of essentially random sequences of nucleotides and amino acids, respectively. Since these random peptides (or nucleic acids, discussed below) are often chemically synthesized, they may inco ⁇ orate a nucleotide or amino acid at any position.
• the synthetic process can be designed to generate randomized proteins or nucleic acids, to allow the formation of all or most ofthe possible combinations over the length ofthe sequence, thus forming a library of randomized candidate bioactive proteinaceous agents.
• the library is fully randomized, with no sequence preferences or constants at any position.
• the library is biased. That is, some positions within the sequence are either held constant, or are selected from a limited number of possibilities.
• the nucleotides or amino acid residues are randomized within a defined class, e.g., of hydrophobic amino acids, hydrophilic residues, sterically biased (either small or large) residues, towards the creation of nucleic acid binding domains, the creation of cysteines, for cross-linking, prolines for SH-3 domains, serines, threonines, tyrosines or histidines for phosphorylation sites, etc.
• a defined class e.g., of hydrophobic amino acids, hydrophilic residues, sterically biased (either small or large) residues, towards the creation of nucleic acid binding domains, the creation of cysteines, for cross-linking, prolines for SH-3 domains, serines, threonines, tyrosines or histidines for phosphorylation sites, etc.
• Modulators of lung cancer can also be nucleic acids, as defined above.
• nucleic acid modulating agents may be naturally occurring nucleic acids, random nucleic acids, or "biased" random nucleic acids. Digests of procaryotic or eucaryotic genomes may be used as is outlined above for proteins.
• the candidate compounds are organic chemical moieties, a wide variety of which are available in the literature.
• the sample containing a target sequence is analyzed.
• the target sequence is prepared using known techniques.
• the sample may be treated to lyse the cells, using known lysis buffers, elecfroporation, etc., with purification and/or amplification such as PCR performed as appropriate.
• an in vitro transcription with labels covalently attached to the nucleotides is performed.
• the nucleic acids are labeled with biotin-FITC or PE, or with cy3 or cy5.
• the target sequence is labeled with, e.g., a fluorescent, a chemiluminescent, a chemical, or a radioactive signal, to provide a means of detecting the target sequence's specific binding to a probe.
• the label also can be an enzyme, such as, alkaline phosphatase or horseradish peroxidase, which when provided with an appropriate substrate produces a product that can be detected.
• the label can be a labeled compound or small molecule, such as an enzyme inhibitor, that binds but is not catalyzed or altered by the enzyme.
• the label also can be a moiety or compound, such as, an epitope tag or biotin which specifically binds to streptavidin.
• the streptavidin is labeled as described above, thereby, providing a detectable signal for the bound target sequence. Unbound labeled streptavidin is typically removed prior to analysis.
• Nucleic acid assays can be direct hybridization assays or can comprise "sandwich assays", which include the use of multiple probes, as is generally outlined in U.S. Patent Nos. 5,681,702, 5,597,909, 5,545,730, 5,594,117, 5,591,584, 5,571,670, 5,580,731, 5,571,670, 5,591,584, 5,624,802, 5,635,352, 5,594,118, 5,359,100, 5,124,246 and 5,681,697, all of which are hereby inco ⁇ orated by reference.
• the target nucleic acid is prepared as outlined above, and then added to the biochip comprising a plurality of nucleic acid probes, under conditions that allow the formation of a hybridization complex.
• hybridization conditions may be used in the present invention, including high, moderate and low stringency conditions as outlined above.
• the assays are generally run under stringency conditions which allow formation ofthe label probe hybridization complex only in the presence of target.
• Stringency can be controlled by altering a step parameter that is a thermodynamic variable, including, but not limited to, temperature, formamide concentration, salt concentration, chaofropic salt concentration, pH, organic solvent concentration, etc.
• the reactions outlined herein may be accomplished in a variety of ways. Components ofthe reaction may be added simultaneously, or sequentially, in different orders, with preferred embodiments outlined below.
• the reaction may include a variety of other reagents. These include salts, buffers, neutral proteins, e.g., albumin, detergents, etc. which may be used to facilitate optimal hybridization and detection, and/or reduce nonspecific or background interactions. Reagents that otherwise improve the efficiency ofthe assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may also be used as appropriate, depending on the sample preparation methods and purity ofthe target.
• the assay data are analyzed to determine the expression levels, and changes in expression levels as between states, of individual genes, forming a gene expression profile.
• Screens are performed to identify modulators ofthe lung cancer phenotype.
• screening is performed to identify modulators that can induce or suppress a particular expression profile, thus preferably generating the associated phenotype.
• screens can be performed to identify modulators that alter expression of individual genes.
• screening is performed to identify modulators that alter a biological function ofthe expression product of a differentially expressed gene. Again, having identified the importance of a gene in a particular state, screens are performed to identify agents that bind and/or modulate the biological activity of the gene product, or evaluate genetic polymo ⁇ hisms.
• Genes can be screened for those that are induced in response to a candidate agent. After identifying a modulator based upon its ability to suppress a lung cancer expression pattern leading to a normal expression pattern, or to modulate a single lung cancer gene expression profile so as to mimic the expression ofthe gene from normal tissue, a screen as described above can be performed to identify genes that are specifically modulated in response to the agent. Comparing expression profiles between normal tissue and agent treated lung cancer tissue reveals genes that are not expressed in normal tissue or lung cancer tissue, but are expressed in agent treated tissue. These agent-specific sequences can be identified and used by methods described herein for lung cancer genes or proteins. In particular these sequences and the proteins they encode find use in marking or identifying agent treated cells.
• a test compound is administered to a population of lung cancer cells, that have an associated lung cancer expression profile.
• minisfration or “contacting” herein is meant that the candidate agent is added to the cells in such a manner as to allow the agent to act upon the cell, whether by uptake and intracellular action, or by action at the cell surface.
• nucleic acid encoding a proteinaceous candidate agent may be put into a viral construct such as an adenoviral or retroviral construct, and added to the cell, such that expression ofthe peptide agent is accomplished, e.g., PCT US97/01019; Regulatable gene therapy systems can also be used.
• a test compound Once a test compound has been administered to the cells, the cells can be washed if desired and are allowed to incubate under preferably physiological conditions for some period of time. The cells are then harvested and a new gene expression profile is generated, as outlined herein.
• lung cancer or non-malignant tissue may be screened for agents that modulate, e.g., induce or suppress a lung cancer phenotype.
• a change in at least one gene, preferably many, ofthe expression profile indicates that the agent has an effect on lung cancer activity.
• screens for new drugs that alter the phenotype can be devised. With this approach, the drug target need not be known and need not be represented in the original expression screening platform, nor does the level of transcript for the target protein need to change.
• Measure of lung cancer polypeptide activity, or of lung cancer or the lung cancer phenotype can be performed using a variety of assays.
• the effects ofthe test compounds upon the function ofthe metastatic polypeptides can be measured by examining parameters described above.
• a suitable physiological change that affects activity can be used to assess the influence of a test compound on the polypeptides of this invention.
• the functional consequences are determined using intact cells or animals, one can also measure a variety of effects such as, in the case of lung cancer associated with tumors, tumor growth, tumor metastasis, neovascularization, hormone release, transcriptional changes to both known and uncharacterized genetic markers (e.g., northern blots), changes in cell metabolism such as cell growth or pH changes, and changes in intracellular second messengers such as cGMP.
• mammalian lung cancer polypeptide is typically used, e.g., mouse, preferably human.
• Assays to identify compounds with modulating activity can be performed in vitro.
• a lung cancer polypeptide is first contacted with a potential modulator and incubated for a suitable amount of time, e.g., from 0.5 to 48 hours.
• the lung cancer polypeptide levels are determined in vitro by measuring the level of protein or mRNA.
• the level of protein is typically measured using immunoassays such as western blotting, ELISA and the like with an antibody that selectively binds to the lung cancer polypeptide or a fragment thereof.
• amplification e.g., using PCR, LCR, or hybridization assays, e.g., northern hybridization, RNAse protection, dot blotting
• hybridization assays e.g., northern hybridization, RNAse protection, dot blotting
• the level of protein or mRNA is typically detected using directly or indirectly labeled detection agents, e.g., fluorescentiy or radioactively labeled nucleic acids, radioactively or enzymatically labeled antibodies, and the like, as described herein.
• a reporter gene system can be devised using a lung cancer protein promoter operably linked to a reporter gene such as luciferase, green fluorescent protein, CAT, or ⁇ -gal.
• the reporter construct is typically transfected into a cell. After treatment with a potential modulator, the amount of reporter gene franscription, translation, or activity is measured according to standard techniques known to those of skill in the art.
• screens may be done on individual genes and gene products (proteins). That is, having identified a particular differentially expressed gene as important in a particular state, screening of modulators ofthe expression of the gene or the gene product itself can be done.
• the gene products of differentially expressed genes are sometimes referred to herein as "lung cancer proteins.”
• the lung cancer protein may be a fragment, or alternatively, be the full length protein to a fragment shown herein.
• screening for modulators of expression of specific genes is performed. Typically, the expression of only one or a few genes are evaluated.
• screens are designed to first find compounds that bind to differentially expressed proteins. These compounds are then evaluated for the ability to modulate differentially expressed activity. Moreover, once initial candidate compounds are identified, variants can be further screened to better evaluate stracture activity relationships.
• binding assays are done.
• purified or isolated gene product is used; that is, the gene products of one or more differentially expressed nucleic acids are made.
• antibodies are generated to the protein gene products, and standard immunoassays are run to determine the amount of protein present.
• cells comprising the lung cancer proteins can be used in the assays.
• the methods comprise combining a lung cancer protein and a candidate compound, and determining the binding ofthe compound to the lung cancer protein.
• Preferred embodiments utilize the human lung cancer protein, although other mammalian proteins may also be used, e.g., for the development of animal models of human disease.
• variant or derivative lung cancer proteins may be used.
• the lung cancer protein or the candidate agent is non-diffusably bound to an insoluble support, preferably having isolated sample receiving areas (e.g., a microtiter plate, an array, etc.).
• the insoluble supports may be made of a composition to which the compositions can be bound, is readily separated from soluble material, and is otherwise compatible with the overall method of screening.
• the surface of such supports may be solid or porous and of a convenient shape.
• suitable insoluble supports include microtiter plates, arrays, membranes and beads. These are typically made of glass, plastic (e.g., polystyrene), polysaccharides, nylon or nitrocellulose, teflonTM, etc. Microtiter plates and arrays are especially convenient because a large number of assays can be carried out simultaneously, using small amounts of reagents and samples.
• the particular manner of binding ofthe composition is typically not cracial so long as it is compatible with the reagents and overall methods ofthe invention, maintains the activity ofthe composition, and is nondiffusable.
• Preferred methods of binding include the use of antibodies (which do not sterically block either the ligand binding site or activation sequence when the protein is bound to the support), direct binding to "sticky" or ionic supports, chemical crosslinking, the synthesis ofthe protein or agent on the surface, etc. Following binding ofthe protein or agent, excess unbound material is removed by washing. The sample receiving areas may then be blocked through incubation with bovine serum albumin (BSA), casein or other innocuous protein or other moiety.
• BSA bovine serum albumin
• the lung cancer protein is bound to the support, and a test compound is added to the assay.
• the candidate agent is bound to the support and the lung cancer protein is added.
• Novel binding agents include specific antibodies, non- natural binding agents identified in screens of chemical libraries, peptide analogs, etc. Of particular interest are screening assays for agents that have a low toxicity for human cells. A wide variety of assays may be used for this pu ⁇ ose, including labeled in vitro protein-protein binding assays, electrophoretic mobility shift assays, immunoassays for protem binding, functional assays (phosphorylation assays, etc.) and the like.
• the determination ofthe binding ofthe test modulating compound to the lung cancer protein may be done in a number of ways.
• the compound is labeled, and bmding determined directly, e.g., by attaching all or a portion ofthe lung cancer protein to a solid support, adding a labeled candidate agent (e.g., a fluorescent label), washing off excess reagent, and determining whether the label is present on the solid support.
• a labeled candidate agent e.g., a fluorescent label
• washing off excess reagent e.g., a fluorescent label
• Various blocking and washing steps may be utilized as appropriate.
• only one ofthe components is labeled, e.g., the proteins (or proteinaceous candidate compounds) can be labeled.
• the binding ofthe test compound is determined by competitive binding assay.
• the competitor may be a binding moiety known to bind to the target molecule (i.e., a lung cancer protein), such as an antibody, peptide, binding partner, ligand, etc. Under certain circumstances, there may be competitive binding between the compound and the binding moiety, with the binding moiety displacing the compound.
• the test compound is labeled.
• Either the compound, or the competitor, or both, is added first to the protein for a time sufficient to allow binding, if present. Incubations may be performed at a temperature which facilitates optimal activity, typically between 4 and 40° C. Incubation periods are typically optimized, e.g., to facilitate rapid high throughput screening. Typically between 0.1 and 1 hour will be sufficient. Excess reagent is generally removed or washed away. The second component is then added, and the presence or absence ofthe labeled component is followed, to indicate binding.
• the competitor is added first, followed by a test compound.
• Displacement ofthe competitor is an indication that the test compound is binding to the lung cancer protein and thus is capable of binding to, and potentially modulating, the activity ofthe lung cancer protein.
• either component can be labeled.
• the presence of label in the wash solution indicates displacement by the agent.
• the test compound is labeled, the presence ofthe label on the support indicates displacement.
• the test compound is added first, with incubation and washing, followed by the competitor.
• the absence of binding by the competitor may indicate that the test compound is bound to the lung cancer protein with a higher affinity.
• the presence ofthe label on the support, coupled with a lack of - competitor binding may indicate that the test compound is capable of binding to the lung cancer protein.
• the methods comprise differential screening to identity agents that are capable of modulating the activity ofthe lung cancer proteins.
• the methods comprise combining a lung cancer protein and a competitor in a first sample.
• a second sample comprises a test compound, a lung cancer protein, and a competitor.
• the binding ofthe competitor is determined for both samples, and a change, or difference in binding between the two samples indicates the presence of an agent capable of binding to the lung cancer protein and potentially modulating its activity. That is, if the binding ofthe competitor is different in the second sample relative to the first sample, the agent is capable of binding to the lung cancer protein.
• differential screening is used to identify drag candidates that bind to the native lung cancer protein, but cannot bind to modified lung cancer proteins.
• the stracture of the lung cancer protein may be modeled, and used in rational drag design to synthesize agents that interact with that site.
• Drug candidates that affect the activity of a lung cancer protein are also identified by screening drugs for the ability to either enhance or reduce the activity of the protein.
• Positive controls and negative controls may be used in the assays.
• confrol and test samples are performed in at least triplicate to obtain statistically significant results. Incubation of all samples is for a time sufficient for the binding ofthe agent to the protein. Following incubation, samples are washed free of non-specifically bound material and the amount of bound, generally labeled agent determined. For example, where a radiolabel is employed, the samples may be counted in a scintillation counter to determine the amount of bound compound.
• reagents may be included in the screening assays. These include reagents like salts, neutral proteins, e.g., albumin, detergents, etc. which may be used to facilitate optimal protein-protein binding and/or reduce non-specific or background interactions. Also reagents that otherwise improve the efficiency ofthe assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may be used. The mixture of components may be added in an order that provides for the requisite binding.
• the invention provides methods for screening for a compound capable of modulating the activity of a lung cancer protein.
• the methods comprise adding a test compound, as defined above, to a cell comprising lung cancer proteins.
• Preferred cell types include almost any cell.
• the cells contain a recombinant nucleic acid that encodes a lung cancer protein.
• a library of candidate agents are tested on a plurality of cells.
• the assays are evaluated in the presence or absence or previous or subsequent exposure of physiological signals, e.g., hormones, antibodies, peptides, antigens, cytokines, growth factors, action potentials, pharmacological agents including chemotherapeutics, radiation, carcinogenics, or other cells (e.g., cell-cell contacts).
• physiological signals e.g., hormones, antibodies, peptides, antigens, cytokines, growth factors, action potentials, pharmacological agents including chemotherapeutics, radiation, carcinogenics, or other cells (e.g., cell-cell contacts).
• the determinations are determined at different stages ofthe cell cycle process.
• a method of inhibiting lung cancer cell division comprises administration of a lung cancer inhibitor.
• a method of inhibiting lung cancer is provided.
• the method may comprise adminisfration of a lung cancer inhibitor.
• methods of treating cells or individuals with lung cancer are provided, e.g., comprising administration of a lung cancer inhibitor.
• a lung cancer inhibitor is an antibody as discussed above. In another embodiment, the lung cancer inhibitor is an antisense molecule.
• a variety of cell growth, proliferation, viability, and metastasis assays are known to those of skill in the art, as described below.
• Soft agar growth or colony formation in suspension Normal cells require a solid substrate to attach and grow. When the cells are transformed, they lose this phenotype and grow detached from the substrate.
• transformed cells can grow in stirred suspension culture or suspended in semi-solid media, such as semi-solid or soft agar.
• the transformed cells when transfected with tumor suppressor genes, regenerate normal phenotype and require a solid subsfrate to attach and grow.
• Soft agar growth or colony formation in suspension assays can be used to identify modulators of lung cancer sequences, which when expressed in host cells, inhibit abnormal cellular proliferation and transformation.
• a therapeutic compound would reduce or eliminate the host cells' ability to grow in stirred suspension culture or suspended in semi-solid media, such as semi-solid or soft.
• Normal cells typically grow in a flat and organized pattern in a petri dish until they touch other cells. When the cells touch one another, they are contact inhibited and stop growing. When cells are transformed, however, the cells are not contact inhibited and continue to grow to high densities in disorganized foci. Thus, the transformed cells grow to a higher saturation density than normal cells. This can be detected mo ⁇ hologically by the formation of a disoriented monolayer of cells or rounded cells in foci within the regular pattern of normal surrounding cells. Alternatively, labeling index with ( H)-thym ⁇ dine at saturation density can be used to measure density limitation of growth. See Freshney (1994), supra. The transformed cells, when transfected with tumor suppressor genes, regenerate a normal phenotype and become contact inhibited and would grow to a lower density.
• labeling index with ( H)-thymidine at saturation density is a preferred method of measuring density limitation of growth.
• Transformed host cells are fransfected with a lung cancer-associated sequence and are grown for 24 hours at saturation density in non-limiting medium conditions.
• the percentage of cells labeling with ( 3 H)-thymidine is determined autoradiographically. See, Freshney (1994), supra.
• Transformed cells typically have a lower serum dependence than their normal counte ⁇ arts (see, e.g., Temin (1966) J. Natl. Cancer Insti. 37:167-175; Eagle, et al. (1970) __ Exp. Med. 131:836-879); Freshney, supra. This is in part due to release of various growth factors by the transformed cells. Growth factor or serum dependence of transformed host cells can be compared with that of control.
• Tumor cells release an increased amount of certain factors (hereinafter "tumor specific markers") than their normal counte ⁇ arts.
• plasminogen activator PA
• Tumor angiogenesis factor TAF
• the degree of invasiveness into Matrigel or some other exfracellular matrix constituent can be used as an assay to identify compounds that modulate lung cancer- associated sequences.
• Tumor cells exhibit a good correlation between malignancy and invasiveness of cells into Matrigel or some other extracellular matrix constituent.
• tumorigenic cells are typically used as host cells. Expression of a tumor suppressor gene in these host cells would decrease invasiveness ofthe host cells. Techniques described in Freshney (1994), supra, can be used. Briefly, the level of invasion of host cells can be measured by using filters coated with Matrigel or some other extracellular matrix constituent. Penetration into the gel, or through to the distal side ofthe filter, is rated as invasiveness, and rated histologically by number of cells and distance
• Knock-out transgenic mice can be made, in which the lung cancer gene is disrupted or in which a lung cancer gene is inserted.
• Knock-out fransgenic mice can be made by insertion of a marker gene or other heterologous gene into the endogenous lung cancer gene site in the mouse genome via homologous recombination. Such mice can also be made by substituting the endogenous lung cancer gene with a mutated version ofthe lung cancer gene, or by mutating the endogenous lung cancer gene, e.g., by exposure to carcinogens.
• a DNA construct is introduced into the nuclei of embryonic stem cells.
• Cells containing the newly engineered genetic lesion are injected into a host mouse embryo, which is re-implanted into a recipient female. Some of these embryos develop into chimeric mice that possess germ cells partially derived from the mutant cell line. Therefore, by breeding the chimeric mice it is possible to obtain a new line of mice containing the introduced genetic lesion (see, e.g., Capecchi, et al. (1989) Science 244:1288).
• Chimeric targeted mice can be derived according to Hogan, et al. (1988) Manipulating the Mouse Embryo: A Laboratory Manual. Cold Spring Harbor Laboratory and Robertson (ed. 1987) Teratocarcinomas and Embryonic Stem Cells: A Practical Approach. , IRL Press, Washington, D.C.
• various immune-suppressed or immune-deficient host animals can be used.
• genetically athymic "nude” mouse see, e.g., Giovanella, et al. (1974) Natl. Cancer Inst. 52:921)
• SCID mouse a SCID mouse
• a thymectomized mouse a thymectomized mouse
• an irradiated mouse see, e.g., Bradley, et al. (1978) Br. J. Cancer 38:263; Selby, et al. (1980) Br. J. Cancer 41:52
• irradiated mouse see, e.g., Bradley, et al. (1978) Br. J. Cancer 38:263; Selby, et al. (1980) Br. J. Cancer 41:52
• Transplantable tumor cells typically about 10 6 cells
• injected into isogenic hosts will produce invasive tumors in a high proportions of cases, while normal cells of similar origin will not.
• cells expressing a lung cancer-associated sequences are injected subcutaneously.
• tumor growth is measured (e.g., by volume or by its two largest dimensions) and compared to the control. Tumors that have statistically significant reduction (using, e.g., Student's T test) are said to have inhibited growth.
• the activity of a lung cancer-associated protein is downregulated, or entirely inhibited, by the use of antisense or an inhibitory polynucleotide, i.e., a nucleic acid complementary to, and which can preferably hybridize specifically to, a coding mRNA nucleic acid sequence, e.g., a lung cancer protein mRNA, or a subsequence thereof. Binding ofthe antisense polynucleotide to the mRNA reduces the franslation and/or stability ofthe mRNA.
• an inhibitory polynucleotide i.e., a nucleic acid complementary to, and which can preferably hybridize specifically to, a coding mRNA nucleic acid sequence, e.g., a lung cancer protein mRNA, or a subsequence thereof. Binding ofthe antisense polynucleotide to the mRNA reduces the franslation and/or stability ofthe mRNA.
• antisense polynucleotides can comprise naturally- occurring nucleotides, or synthetic species formed from naturally-occurring subunits or their close homologs. Antisense polynucleotides may also have altered sugar moieties or inter- sugar linkages. Exemplary among these are the phosphorothioate and other sulfur containing species which are known for use in the art. Analogs are comprehended by this invention so long as they function effectively to hybridize with the lung cancer protein mRNA. See, e.g., Isis Pharmaceuticals, Carlsbad, CA; Sequitor, Inc., Natick, MA.
• antisense polynucleotides can readily be synthesized using recombinant means, or can be synthesized in vitro. Equipment for such synthesis is sold by several vendors, including Applied Biosystems. The preparation of other oligonucleotides such as phosphorothioates and alkylated derivatives is also well known to those of skill in the art.
• Antisense molecules as used herein include antisense or sense oligonucleotides. Sense oligonucleotides can, e.g., be employed to block franscription by binding to the anti- sense strand.
• the antisense and sense oligonucleotide comprise a single-stranded nucleic acid sequence (either RNA or DNA) capable of binding to target mRNA (sense) or DNA (antisense) sequences for lung cancer molecules.
• a preferred antisense molecule is for a lung cancer sequence in the tables, or for a ligand or activator thereof.
• Antisense or sense oligonucleotides, according to the present invention comprise a fragment generally at least about 14 nucleotides, preferably from about 14 to 30 nucleotides.
• RNA interference is a mechanism to suppress gene expression in a sequence specific manner. See, e.g., Bramelkamp, et al. (2002) Sciencexpress (21March2002); Sha ⁇ (1999) Genes Dev. 13:139-141; and Cathew (2001) Curr. Op. Cell Biol. 13:244-248.
• short e.g., 21 nt
• double sfranded small interfering RNAs siRNA
• the mechanism may be used to downregulate expression levels of identified genes, e.g., treatment of or validation of relevance to disease.
• ribozymes can be used to target and inhibit transcription of lung cancer-associated nucleotide sequences.
• a ribozyme is an RNA molecule that catalytically cleaves other RNA molecules.
• Different kinds of ribozymes have been described, including group I ribozymes, hammerhead ribozymes, hai ⁇ in ribozymes, RNase P, and axhead ribozymes (see, e.g., Castanotto, et al. (1994) Adv. in Pharmacology 25: 289-317 for a general review ofthe properties of different ribozymes).
• hai ⁇ in ribozymes are described, e.g., in Hampel, et al. (1990) Nucl. Acids Res. 18:299-304; European Patent Publication No. 0 360 257; U.S. Patent No. 5,254,678.
• Methods of preparing are well known to those of skill in the art (see, e.g., WO 94/26877; Ojwang, et al. (1993) Proc. Natl. Acad. Sci. USA 90:6340-6344; Yamada, et al. (1994) Human Gene Therapy 1:39-45; Leavitt, et al. (1995) Proc. Natl. Acad. Sci.
• Polynucleotide modulators of lung cancer may be introduced into a cell containing the target nucleotide sequence by formation of a conjugate with a ligand binding molecule, as described in WO 91/04753.
• Suitable ligand binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to cell surface receptors.
• conjugation ofthe ligand binding molecule does not substantially interfere with the ability ofthe ligand binding molecule to bind to its corresponding molecule or receptor, or block entry ofthe sense or antisense oligonucleotide or its conjugated version into the cell.
• a polynucleotide modulator of lung cancer may be introduced into a cell containing the target nucleic acid sequence, e.g., by formation of an polynucleotide-lipid complex, as described in WO 90/10448. It is understood that the use of antisense molecules or knock out and knock in models may also be used in screening assays as discussed above, in addition to methods of freatment.
• methods of modulating lung cancer in cells or organisms comprise administering to a cell an anti-lung cancer antibody that reduces or eliminates the biological activity of an endogenous lung cancer protein.
• the methods comprise administering to a cell or organism a recombinant nucleic acid encoding a lung cancer protein. This may be accomplished in any number of ways. In a prefened embodiment, e.g., when the lung cancer sequence is down- regulated in lung cancer, such state may be reversed by increasing the amount of lung cancer gene product in the cell. This can be accomplished, e.g., by overexpressing the endogenous lung cancer gene or administering a gene encoding the lung cancer sequence, using known gene-therapy techniques.
• the gene therapy techniques include the inco ⁇ oration ofthe exogenous gene using enhanced homologous recombination (EHR), e.g., as described in PCT/US93/03868, hereby inco ⁇ orated by reference in its entirety.
• EHR enhanced homologous recombination
• the lung cancer sequence when the lung cancer sequence is up-regulated in lung cancer, the activity ofthe endogenous lung cancer gene is decreased, e.g., by the administration of a lung cancer antisense or RNAi nucleic acid.
• the lung cancer proteins ofthe present invention may be used to generate polyclonal and monoclonal antibodies to lung cancer proteins.
• the lung cancer proteins can be coupled, using standard technology, to affinity chromatography columns. These columns may then be used to purify lung cancer antibodies useful for production, diagnostic, or therapeutic pu ⁇ oses.
• the antibodies are generated to epitopes unique to a lung cancer protein; that is, the antibodies show little or no cross-reactivity to other proteins.
• the lung cancer antibodies may be coupled to standard affinity chromatography columns and used to purify lung cancer proteins.
• the antibodies may also be used as blocking polypeptides, as outlined above, since they will specifically bind to the lung cancer protein.
• the invention provides methods for identifying cells containing variant lung cancer genes, e.g., determining all or part ofthe sequence of at least one endogenous lung cancer genes in a cell.
• the invention provides methods of identifying the lung cancer genotype of an individual, e.g., determining all or part ofthe sequence of at least one lung cancer gene ofthe individual. This is generally done in at least one tissue ofthe individual, and may include the evaluation of a number of tissues or different samples ofthe same tissue.
• the method may include comparing the sequence ofthe sequenced lung cancer gene to a known lung cancer gene, i.e., a wild-type gene.
• the sequence of all or part ofthe lung cancer gene can then be compared to the sequence of a known lung cancer gene to determine if any differences exist. This can be done using known homology programs, such as Bestfit, etc.
• the presence of a difference in the sequence between the lung cancer gene ofthe patient and the known lung cancer gene conelates with a disease state or a propensity for a disease state, as outlined herein.
• the lung cancer genes are used as probes to determine the number of copies ofthe lung cancer gene in the genome.
• the lung cancer genes are used as probes to determine the chromosomal localization ofthe lung cancer genes.
• Information such as chromosomal localization finds use in providing a diagnosis or prognosis in particular when chromosomal abnormalities such as translocations, and the like are identified in the lung cancer gene locus.
• a therapeutically effective dose of a lung cancer protein or modulator thereof is administered to a patient.
• therapeutically effective dose herein is meant a dose that produces effects for which it is administered. The exact dose will depend on the pu ⁇ ose ofthe treatment, and will be ascertainable by one skilled in the art using known techniques (e.g., Ansel, et al. (1992) Pharmaceutical Dosage Forms and Drug Delivery: Lieberman, Pharmaceutical Dosage Forms (vols. 1-3), Dekker, ISBN 0824770846, 082476918X, 0824712692, 0824716981; Lloyd (1999) The Art. Science and Technology of Pharmaceutical Compounding; and Pickar (1999) Dosage Calculations).
• a "patient” for the pu ⁇ oses ofthe present invention includes both humans and other animals, particularly mammals. Thus the methods are applicable to both human therapy and veterinary applications.
• the patient is a mammal, preferably a primate, and in the most prefened embodiment the patient is human.
• the adminisfration ofthe lung cancer proteins and modulators thereof of the present invention can be done in a variety of ways, including, but not limited to, orally, subcutaneously, intravenously, infranasally, transdermaUy, infraperitoneally, intramuscularly, mtrapulmonary, vaginally, rectally, or infraocularly.
• the lung cancer proteins and modulators may be directly applied as a solution or spray.
• compositions ofthe present invention comprise a lung cancer protein in a form suitable for administration to a patient.
• the pharmaceutical compositions are in a water soluble form, such as being present as pharmaceutically acceptable salts, which is meant to include both acid and base addition salts.
• “Pharmaceutically acceptable acid addition salt” refers to those salts that retain the biological effectiveness ofthe free bases and that are not biologically or otherwise undesirable, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid and the like.
• inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like
• organic acids such as acetic acid, propionic acid, glycolic acid, pyruvic acid,
• “Pharmaceutically acceptable base addition salts” include those derived from inorganic bases such as sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Particularly prefened are the ammonium, potassium, sodium, calcium, and magnesium salts. Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine.
• compositions may also include one or more ofthe following: carrier proteins such as serum albumin; buffers; fillers such as microcrystalline cellulose, lactose, corn and other starches; binding agents; sweeteners and other flavoring agents; coloring agents; and polyethylene glycol.
• the pharmaceutical compositions can be administered in a variety of unit dosage forms depending upon the method of administration.
• unit dosage forms suitable for oral administration include, but are not limited to, powder, tablets, pills, capsules and lozenges.
• lung cancer protein modulators e.g., antibodies, antisense constructs, ribozymes, small organic molecules, etc.
• This is typically accomplished either by complexing the molecule(s) with a composition to render it resistant to acidic and enzymatic hydrolysis, or by packaging the molecule(s) in an appropriately resistant carrier, such as a liposome or a protection barrier.
• Means of protecting agents from digestion are well known in the art.
• compositions for administration will commonly comprise a lung cancer protein modulator dissolved in a pharmaceutically acceptable carrier, preferably an aqueous carrier.
• a pharmaceutically acceptable carrier preferably an aqueous carrier.
• aqueous carriers can be used, e.g., buffered saline and the like. These solutions are sterile and generally free of undesirable matter.
• These compositions may be sterilized by conventional, well known sterilization techniques.
• the compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, e.g., sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like.
• a typical pharmaceutical composition for intravenous administration would be about 0.1 to 10 mg per patient per day. Dosages from 0.1 up to about 100 mg per patient per day may be used, particularly when the drag is administered to a secluded site and not into the blood stream, such as into a body cavity or into a lumen of an organ. Substantially higher dosages are possible in topical adminisfration. Actual methods for preparing parenterally administrable compositions will be known or apparent to those skilled in the art, e.g.,
• compositions containing modulators of lung cancer proteins can be administered for therapeutic or prophylactic treatments.
• compositions are administered to a patient suffering from a disease (e.g., a cancer) in an amount sufficient to cure or at least partially anest the disease and its complications.
• An amount adequate to accomplish this is defined as a "therapeutically effective dose.” Amounts effective for this use will depend upon the severity ofthe disease and the general state ofthe patient's health.
• Single or multiple administrations ofthe compositions may be administered depending on the dosage and frequency as required and tolerated by the patient. In any event, the composition should provide a sufficient quantity ofthe agents of this invention to effectively freat the patient.
• An amount of modulator that is capable of preventing or slowing the development of cancer in a mammal is refened to as a "prophylactically effective dose.”
• the particular dose required for a prophylactic treatment will depend upon the medical condition and history of the mammal, the particular cancer being prevented, as well as other factors such as age, weight, gender, administration route, efficiency, etc.
• Such prophylactic treatments may be used, e.g., in a mammal who has previously had cancer to prevent a recunence ofthe cancer, or in a mammal who is suspected of having a significant likelihood of developing cancer based, at least in part, upon gene expression profiles.
• Vaccine strategies may be used, in either a DNA vaccine form, or protein vaccine.
• lung cancer protein-modulating compounds can be administered alone or in combination with additional lung cancer modulating compounds or with other therapeutic agent, e.g., other anti-cancer agents or treatments.
• one or more nucleic acids e.g., polynucleotides comprising nucleic acid sequences set forth in the tables, such as antisense or RNAi polynucleotides or ribozymes, will be introduced into cells, in vitro or in vivo.
• the present invention provides methods, reagents, vectors, and cells useful for expression of lung cancer- associated polypeptides and nucleic acids using in vitro (cell-free), ex vivo, or in vivo (cell or organism-based) recombinant expression systems.
• the particular procedure used to introduce the nucleic acids into a host cell for expression of a protein or nucleic acid is application specific. Many procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, spheroplasts, electroporation, liposomes, microinjection, plasma vectors, viral vectors and other well known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see, e.g., Berger and Kimmel, Guide to Molecular Cloning Techniques. Methods in Enzymology volume 152 (Berger), Ausubel, et al. (eds.
• lung cancer proteins and modulators are administered as therapeutic agents, and can be formulated as outlined above.
• lung cancer genes can be administered in a gene therapy application. These lung cancer genes can include antisense or inhibitory applications, e.g., as inhibitory RNA or gene therapy (e.g., for inco ⁇ oration into the genome) or as antisense compositions.
• Lung cancer polypeptides and polynucleotides can also be administered as vaccine compositions to stimulate HTL, CTL, and antibody responses.
• Such vaccine compositions can include, e.g., lipidated peptides (see, e.g.,Vitiello, et al. (1995) J. Clin. Invest. 95:341), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) ("PLG”) microspheres (see, e.g., Eldridge, et al. (1991) Molec. Immunol. 28:287-294; Alonso, et al. (1994) Vaccine 12:299-306; Jones, et al.
• Vaccine 13:675-681 peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi, et al. (1990) Nature 344:873-875; Hu, et al. (1998) Clin Exp Immunol. 113:235-243), multiple antigen peptide systems (MAPs) (see, e.g., Tarn (1988) Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413; Tarn (1996) J. Immunol.
• ISCOMS immune stimulating complexes
• MAPs multiple antigen peptide systems
• Toxin-targeted delivery technologies also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Massachusetts) may also be used.
• Vaccine compositions often include adjuvants.
• Many adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium tuberculosis derived proteins.
• adjuvants are commercially available as, e.g., Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, MI); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, NJ); AS-2 (SmithKline Beecham, Philadelphia, PA); aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quil A.
• Freund's Incomplete Adjuvant and Complete Adjuvant Difco Laboratories, Detroit, MI
• Merck Adjuvant 65 Merck and Company, Inc., Rahway, NJ
• AS-2 SmithKline Beecham, Philadelphia, PA
• aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate
• Cytokines such as GM-CSF, interleukin-2, -7, -12, and other like growth factors, may also be used as adjuvants.
• Vaccines can be administered as nucleic acid compositions wherein DNA or RNA encoding one or more ofthe polypeptides, or a fragment thereof, is administered to a patient. This approach is described, for instance, in Wolff, et. al. (1990) Science 247:1465 as well as U.S. Patent Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720; and in more detail below.
• DNA-based delivery technologies include "naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g., U.S. Patent No. 5,922,687).
• the peptides ofthe invention can be expressed by viral or bacterial vectors.
• expression vectors include attenuated viral hosts, such as vaccinia or fowlpox. This approach involves the use of vaccinia virus, e.g., as a vector to express nucleotide sequences that encode lung cancer polypeptides or polypeptide fragments. Upon introduction into a host, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits an immune response.
• Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Patent No. 4,722,848.
• BCG Bacille Cahnette Guerin
• BCG vectors are described in Stover, et al. (1991) Nature 351:456-460.
• a wide variety of other vectors useful for therapeutic administration or immunization e.g., adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein (see, e.g., Shata, et al. (2000) Mol Med Today 6:66-71; Shedlock, et al. (2000) J. Leukoc. Biol. 68:793-806; Hipp, et al. (2000) In Vivo 14:571-85).
• Methods for the use of genes as DNA vaccines are well known, and include placing a lung cancer gene or portion of a lung cancer gene under the control of a regulatable promoter or a tissue-specific promoter for expression in a lung cancer patient.
• the lung cancer gene used for DNA vaccines can encode full-length lung cancer proteins, but more preferably encodes portions ofthe lung cancer proteins including peptides derived from the lung cancer protein.
• a patient is immunized with a DNA vaccine comprising a plurality of nucleotide sequences derived from a lung cancer gene.
• lung cancer- associated genes or sequence encoding subfragments of a lung cancer protein are introduced into expression vectors and tested for their immunogenicity in the context of Class I MHC and an ability to generate cytotoxic T cell responses. This procedure provides for production of cytotoxic T cell responses against cells which present antigen, including intracellular epitopes.
• DNA vaccines include a gene encoding an adjuvant molecule with the DNA vaccine.
• adjuvant molecules include cytokines that increase the immunogenic response to the lung cancer polypeptide encoded by the DNA vaccine. Additional or alternative adjuvants are available.
• lung cancer genes find use in generating animal models of lung cancer. When the lung cancer gene identified is repressed or diminished in metastatic tissue, gene therapy technology, e.g., wherein antisense or inhibitory RNA directed to the lung cancer gene will also diminish or repress expression ofthe gene. Animal models of lung cancer find use in screening for modulators of a lung cancer-associated sequence or modulators of lung cancer.
• transgenic animal technology including gene knockout technology, e.g., as a result of homologous recombination with an appropriate gene targeting vector, will result in the absence or increased expression ofthe lung cancer protein.
• tissue-specific expression or knockout ofthe lung cancer protein may be necessary. It is also possible that the lung cancer protein is overexpressed in lung cancer. As such, transgenic animals can be generated that overexpress the lung cancer protein.
• promoters of various strengths can be employed to express the transgene.
• the number of copies ofthe integrated fransgene can be determined and compared for a determination ofthe expression level ofthe fransgene. Animals generated by such methods will find use as animal models of lung cancer and are additionally useful in screening for modulators to freat lung cancer.
• kits for Use in Diagnostic and/or Prognostic Applications
• kits may include at least one ofthe following: assay reagents, buffers, lung cancer-specific nucleic acids or antibodies, hybridization probes and/or primers, antisense polynucleotides, ribozymes, RNAi, dominant negative lung cancer polypeptides or polynucleotides, small molecule inhibitors of lung cancer-associated sequences, etc.
• a therapeutic product may include sterile saline or another pharmaceutically acceptable emulsion and suspension base.
• kits may include instructional materials containing instructions (e.g., protocols) for the practice ofthe methods of this invention. While the instructional materials typically comprise written or printed materials they are not limited to such.
• a medium capable of storing such instructions and communicating them to an end user is contemplated by this invention. Such media include, but are not limited to electronic storage media (e.g., magnetic discs, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. Such media may include addresses to internet sites that provide such instructional materials.
• the present invention also provides for kits for screening for modulators of lung cancer-associated sequences. Such kits can be prepared from readily available materials and reagents.
• kits can comprise one or more ofthe following materials: a lung cancer-associated polypeptide or polynucleotide, reaction tubes, and instructions for testing lung cancer-associated activity.
• the kit contains biologically active lung cancer protein.
• kits and components can be prepared according to the present invention, depending upon the intended user ofthe kit and the particular needs ofthe user. Diagnosis would typically involve evaluation of a plurality of genes or products. The genes typically will be selected based on conelations with important parameters in disease which may be identified in historical or outcome data.
• Tables 1A and 1B were previously filed on April 18, 2001 in USSN 60/284,770 (18501-001500US) and on November 29, 2001 in USSN 60/334,370 (18501-001520US)

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