| Methods for identifying functionally related genes and drug targets -> Monitor Keywords |
|
|
 
Methods for identifying functionally related genes and drug targetsMethods for identifying functionally related genes and drug targets description/claimsThe Patent Description & Claims data below is from USPTO Patent Application 20090263790, Methods for identifying functionally related genes and drug targets. Brief Patent Description - Full Patent Description - Patent Application Claims
This application is a continuation of U.S. patent application Ser. No. 10/309,788, filed on Dec. 4, 2002, which is a continuation-in-part of U.S. patent application Ser. No. 09/750,401, filed on Dec. 28, 2000, now issued as U.S. Pat. No. 6,635,422, which claims the benefit of U.S. Provisional Application Ser. No. 60/173,338, filed Dec. 28, 1999, all of which are hereby incorporated by reference in their entirety. This invention was made with government support under grant number R01 CA79907 from the National Institutes of Health. The United States Government has certain rights in this invention The invention provides methods and compositions for identifying and characterizing functionally related gene products that are associated with mRNA-protein (mRNP) complexes and for characterizing cellular gene expression. The invention also provides methods and compositions for identifying and characterizing therapeutic targets and therapeutics. Most genes are regulated by a complex array of interactions, resulting in unique gene expression patterns. Such gene expression patterns vary between different cell types, cells at different developmental stages or differentiation states, and cells exposed to signaling molecules, stress, infection, or other cellular condition or disorder. Efforts to understand the processes that regulate variant gene expression patterns have concentrated on early events in transcription regulation and in events surrounding translation. In contrast, much less attention has been paid to the role of mRNA-protein complexes (mRNP complexes) in post-transcriptional regulatory processes, such as the regulation of stability, localization, and translation efficiency of mRNAs. Still less is known about the post-transcriptional processes that coordinate the expression of functionally related genes (e.g., genes that share or participate in a certain function or pathway), which are often co-localized to particular mRNP complexes and bound to the same RNA binding protein (RBP). Post-transcriptional gene regulation of some mRNAs is mediated by regulatory elements or sequences that reside in both the introns and exons of pre-mRNAs, and the coding and noncoding regions of mature transcripts. One example of such a regulatory element is the AU-rich instability element (ARE) present in the 3′-untranslated regions (UTRs) of early-response gene mRNAs, many of which encode proteins essential for growth and differentiation. RNA binding proteins associated with mRNP complexes bind to AREs in vitro and mediate post-transcriptional mRNA stability and translation in vivo. However, not all mRNAs that bind to an RNA binding protein possess an ARE or other common regulatory element. Moreover, the mechanism(s) by which an RNA binding protein recognizes mRNAs that do not contain an ARE is not known. In vitro binding assays using RNA binding proteins have shown that the mRNAs that are associated with a particular RNA binding protein are often structurally or functionally related. However, these in vitro methods do not reflect the dynamic nature of mRNA association with mRNP complexes in vivo, which changes in response to intra- and inter- cellular signaling events. A need therefore exists for reliable methods for monitoring RNA binding protein-mRNA interactions, as well as the association of mRNAs and proteins with mRNP complexes in vivo. The use of such methods will allow for the characterization of mRNA-protein interactions and their functional implications, will elucidate biological pathways, and will further allow for the identification of therapeutic targets and therapeutics. The invention provides methods and compositions that are used to identify, utilize, and characterize mRNP complexes to identify functionally related gene products that are coordinately expressed and associated with a particular mRNP complex. The gene products associated with a particular mRNP complex are classified into biologically relevant subsets on the basis of structural and/or functional relationships. These gene products, including mRNAs, RNA binding proteins, other mRNP complex-associated proteins, may participate in a particular biological pathway, such as an enzyme pathway, or may participate in other cellular event or pathology, such as tumor growth, apoptosis, differentiation, aging, or cell toxicity, for example. The functionally and structurally related gene products that are identified and quantified create a ribonomic profile for the cell or population of cells. This ribonomic profile provides a snapshot of the flow of genetic information at a given time in the life of the cell or cell population, in a normal or diseased state, or in response to an environmental influence or drug. The ribonomic profile is used as a diagnostic marker for disease or other cellular event and to rapidly identify therapeutic targets and therapeutics that alter the expression of one or more of the mRNP complex-associated gene products. The identified gene products themselves are also used as diagnostic and therapeutic indicators. For example, the invention provides methods for diagnosing a disease or risk of disease, as well as monitoring a disease state, by identifying and monitoring changes in the expression of mRNP complex-associated gene products in a subject\'s cell sample and comparing the gene expression to that of a normal subject or other non-diseased cell sample. For example, the invention is useful for assessing the cell types present in a population of cells, such as in a tumor, biopsy, or body fluid, by comparing the ribonomic profile of a cell sample to signature RNP profiles characteristic of certain cell types. The identification of certain cell types is useful for diagnosing a tumor or other cellular pathology and for indicating a treatment regimen. The invention provides useful methods for identifying a therapeutic target by contacting a cell sample with a test compound, isolating mRNP complexes, and identifying an mRNP complex component whose expression is altered in response to the compound. The therapeutic target may be any component of the RNP complex or a gene or RNA encoding the component. For example, the RNAs isolated from an RNP complex may be used to probe nucleic acid arrays to identify which genes are affected by the test compound. The invention also provides methods for assessing the efficacy of a test compound as a therapeutic. A cell sample is contacted with a test compound and the mRNP complexes of the cell sample are used to prepare a ribonomic profile that demonstrates changes in expression of gene products associated with the mRNP complexes. A difference in the level of expression of the gene products in the treated cell sample compared to the levels in an untreated cell sample is indicative that the test compound is a candidate therapeutic. The invention may also be used to determine the toxicity of a test compound and to identify genes that participate in cell death. Toxicity can be determined by treating a cell sample with different doses of a test compound, as described above. An array containing nucleic acids that encode regulatory molecules, such as transcription factors, is probed using the RNA isolated from a particular RNP complex, in order to identify the transcription factors, RNA binding proteins, or any other transcriptional, post-transcriptional, translational, or post-translational regulator whose expression is altered in the presence of specific toxicants, in order to identify downstream genes affected by changes in these regulators. Continue reading about Methods for identifying functionally related genes and drug targets... Full patent description for Methods for identifying functionally related genes and drug targets Brief Patent Description - Full Patent Description - Patent Application Claims Click on the above for other options relating to this Methods for identifying functionally related genes and drug targets patent application. Patent Applications in related categories: 20090298077 - Assay for measurement of apurinic/apyrimidinic (ap) sites and for screening ap-site reactive compounds - A method of detecting abasic (AP) sites in DNA from a subject includes isolating a sample of DNA from a subject under examination, contacting the DNA with a fluorescent aldehyde reactive probe (FARP), and detecting FARP labeled AP sites in the DNA sample. ... 20090298082 - Biomarker panels for predicting prostate cancer outcomes - This document provides methods and materials related to assessing male mammals (e.g., humans) with prostate cancer. For example, methods and materials for predicting (1) which patients, at the time of PSA reoccurrence, will later develop systemic disease, (2) which patients, at the time of retropubic radial prostatectomy, will later develop ... 20090298075 - Compositions and methods for nucleic acid sequencing - Compositions and methods for nucleic acid sequencing include template constructs that comprise double stranded portions in a partially or completely contiguous constructs, to provide for redundant sequence determination through one or both of sequencing sense and antisense strands, and iteratively sequencing the entire construct multiple times. Additional sequence components are ... 20090298085 - Detection of extracellular tumor-associated nucleic acid in blood plasma or serum using nucleic acid amplification assays - This invention relates to detection of specific extracellular nucleic acid in plasma or serum fractions of human or animal blood associated with neoplastic or proliferative disease. Specifically, the invention relates to detection of nucleic acid derived from mutant oncogenes or other tumor-associated DNA, and to those methods of detecting and ... 20090298076 - Detection of salmonella by real-time multiplex pcr - The invention relates to the detection of Salmonella by nucleic acid amplification. The invention provides primer and probe oligonucleotides that can be used in multiplex to detect Salmonella in real-time amplification. The oligonucleotides of the invention detect all group I serovars, and have an increased Salmonella detection range: they enable ... 20090298067 - Devices and methods for detecting cells and other analytes - The invention features methods, devices, and kits for the isolation of analytes (e.g., a cell). A sample containing a desired analyte is introduced into a microfluidic device containing moieties that bind the desired analyte. A shear stress is applied that is great enough to prevent binding of undesired analytes and ... 20090298052 - Diagnosing or predicting the course of breast cancer - A method of diagnosing the presence or predicting the course of breast cancer by measuring the expression of a combination of Marker genes comprising a tissue-specific gene and a non-tissue specific gene in a cell or tissue sample derived from a patient. In one aspect of the invention, the genes ... 20090298061 - Diagnostic methods for the prediction of therapeutic success, recurrence free and overall survival in cancer therapy - Described are 12 human genes which are differentially expressed in neoplastic tissues of patients responding well to treatment as compared to patients not responding well as determined by overall survival time in the non responding cohort. Moreover, methods for prognosis of the therapeutic success in cancer therapy are described. These ... 20090298072 - Dna sequencing by nanopore using modified nucleotides - This invention provides a process for sequencing single-stranded DNA by employing a nanopore and modified nucleotides. ... 20090298054 - Epigenetic methods and nucleic acids for the detection of breast cell proliferative disorders - The present application provides methods and nucleic acids for the detection and differentiation of breast cell proliferative disorders. This is achieved by the analysis of the methylation of a panel of genes, or subsets thereof. The invention may be used for the detection and/or differentiation of a variety of tissue ... 20090298084 - Gene and protein expression profiles associated with the therapeutic efficacy of irinotecan - The present invention includes gene and protein expression profiles indicative of whether a cancer patient is likely to respond to treatment with irinotecan. By identifying such responsiveness, a treatment provider may determine in advance those patients who would benefit from such treatment, as well as identify alternative therapies for non-responders. ... 20090298064 - Genomic sequencing - Genomic sequencing is implemented for high throughput applications that can include short reads. In one example, whole-genome sequencing involves a method in which a subset of fragments of a target genome are selected as a random function, and each fragment is replicated into clones. The clones are ordered into clone ... 20090298079 - High affinity binding site of hgfr and methods for identification of antagonists thereof - Use of a polynucleotide encoding or a polypeptide comprising at least the extracellular IPT-3 and IPT-4 domains of hepatocyte growth factor receptor for the screening and/or development of pharmacologically active agents useful in the treatment of cancer, preferably a cancer with dysregulation of hepatocyte growth factor receptor. ... 20090298063 - Il-1 gene cluster and associated inflammatory polymorphisms and haplotypes - The invention provides methods and compositions relating to identification and use of genetic information from the IL-1 gene cluster—including the structure and organization of novel IL-1-like genes found within the IL-1 locus as well as polymorphisms and associated haplotypes within these genes. The invention thereby expands the repertoire of useful ... 20090298058 - Inhibitors of pghs-2transactivator activity - Prostaglandin-endoperoxide H synthase (PGHS-2) converts arachidonic acid to prostaglandin H2. PGHS-2 is an inducible gene product undetectable in most normal human tissues, but abundant in cancer cells. The present invention exploits a previously undisclosed transcriptional function of PGHS-2 distinct from its well-established enzymatic role to identify potential therapeutic agents useful ... 20090298073 - Kidney toxicity biomarkers - Novel biomarkers for kidney toxicity. Said biomarkers may be useful for optimization of lead compounds, or in safety assessment. ... 20090298068 - Method and test kit for the diagnosis and/or making predictions about and/or for the assessment of the efficacy of therapeutic agents for the treatment of ovarian cancer and method of planning a regimen for the treatment of ovarian cancer - The invention relates to a method and a test kit for diagnosing ovarian cancer and/or making predictions in case of ovarian cancer as well as a method for estimating the effectiveness of therapeutic agents during the treatment of ovarian cancer, the promoter hypermethylation of the TUSC3 marker in a biological ... 20090298070 - Method for analyzing metabolites flux using converging ratio determinant and split ratio determinant - The present invention relates to a method for analyzing metabolic flux using CRD and SRD. Specifically, the method comprising: selecting a specific target organism, constructing the metabolic network model of the selected organism, identifying the correlations between specific metabolic fluxes in the metabolic network model, defining the correlation ratios as ... 20090298062 - Method for determination of the length of the g-tail sequence and kit for the method - A method of measuring the length of a G tail sequence, characterized by hybridizing the G tail of an nondenatured chromosomal DNA in a sample with a labeled DNA probe having a sequence complementary to the telomere repeat sequence, measuring chemiluminescence from the hybridized DNA probe, and determining the length ... 20090298071 - Method for testing drug sensitivity in solid tumors by quantifying mrna expression in thinly-sliced tumor tissue - A method is disclosed for assaying the sensitivity of neoplastic tissue to therapeutic agents, and in particular, for the quantification of pro-apoptotic marker mRNA expression in cells obtained from thinly-sliced living tumor tissue in such methods. The method may comprise ascertaining a particular apoptosis marker mRNA for an individual tumor ... 20090298078 - Method for the detection of an activation of the immune system or the extent of cell death - The present invention relates to a method for the detection of an activation of the immune system, preferably in the sense of an NET formation, or the extent of cell death in a non-tumorous tissue or in a body fluid, wherein free DNA is measured in a sample from an ... 20090298056 - Method of identifying cd4+ t cell antigens - The present invention is directed to a method of identifying CD4+ T cell antigens as well as to antigens which were identified by such a method. The present invention further is directed to the application of those identified antigens in medicine. ... 20090298087 - Methods and probes for the detection of cancer - Probe sets and methods of using probes and probe sets for the detection of cancer are described. Methods for detecting cancer that include hybridizing a set of chromosomal probes to a biological sample obtained from a patient, and identifying if cancer cells are present the sample. Also included are methods ... 20090298080 - Methods and reagents for detecting cpg methylation with a methyl cpg binding protein (mbp) - The present invention provides a simple and sensitive technology for the detection of CpG methylation in DNA without chemical modification of sample DNA by bisulfite treatment or PCR amplification. Signal generation is based on an Abscription (Abortive Transcription) technology in which DNA signal generators called Abortive Promoter Cassettes (APCs) are ... 20090298060 - Methods for diagnosing and monitoring the status of systemic lupus erythematosus - The invention presents a method of diagnosing or monitoring the status of systemic lupus erythematosus (SLE) in a subject or patient comprising detecting the expression of all genes of a diagnostic set in the subject or patient wherein the diagnostic set comprises two or more genes having expression correlated with ... 20090298065 - Methods for identifying functional noncoding sequences - The present invention relates to methods for identifying functional noncoding human sequences. Methods may comprise one or more of the following: a comparative genomic sequence analysis step, a genetic analysis step, and a functional analysis step. The functional analysis step comprises transposon-based transgenesis in zebrafish. Also disclosed here in a ... 20090298081 - Methods of treatment utilizing binding proteins of the interleukin-21 receptor - The present invention provides binding proteins and antigen-binding fragments thereof, including human antibodies, that specifically bind to the human interleukin-21 receptor (IL-21R), and methods of using them. The binding proteins can act as, e.g., antagonists of IL-21R activity, thereby modulating immune responses in general, and those mediated by IL-21R in ... 20090298074 - Modulators of elovl5 for treating acne or hyperseborrhea - An in vitro method for screening candidate compounds for the preventive or curative treatment of acne, includes the determination of the capacity of a compound to modulate the expression or the activity of ELOVL5 and the use of modulators of the expression or activity of this enzyme for the treatment ... 20090298083 - Phospho-specific anti-pax3 antibodies - Pax3, a member of the paired class homeodomain family of transcription factors and an essential protein for early skeletal muscle development, was shown to be phosphorylated in proliferating mouse primary myoblasts. Furthermore, Ser205, Ser201 and Ser209 were identified as the only sites of phosphorylation on Pax3 in proliferating mouse primary ... 20090298086 - Plant farnesyltransferases - This invention relates to an isolated nucleic acid fragment encoding a farnesyltransferase subunit. The invention also relates to the construction of a chimeric gene encoding all or a portion of the farnesyltransferase subunit, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels ... 20090298057 - Primer and probe for use in detection of mycobacterium kansasii and method for detection of mycobacterium kansasii using the same - The method for detecting Mycobacterium kansasii enables the detection of M. kansasii more rapidly and with higher accuracy compared with a conventional bacterium identification method performed by culture examination on a bacterium. Further, the method can exclude any false positive result for the diagnosis and can also detect and diagnose ... 20090298069 - Probe, probe set, probe-immobilized carrier, and genetic testing method - A nucleic acid probe for classification of pathogenic bacterial species is capable of collectively detecting bacterial strains of the same species and differentially detecting them from other bacterial species. Any one of the base sequences of SEQ ID NOS. 38 and 39 or a combination of at least two of ... 20090298055 - Production of proteins - The present invention is of a method of producing proteins in mammalian cells using a permanent selection in the absence of cytotoxic drugs. Specifically, the present invention can be used to produce large quantities of highly pure human proteins which are suitable for pharmaceutical applications. ... 20090298066 - Sex-specific marker for shrimps and prawns - The present invention relates to a sex-specific marker for shrimps and prawns. More specifically, it relates to a sex-specific PCR-based molecular marker, derived from Penaeus monodon, that can be used to determine the sex in shrimps and prawns and can be used for any and all requirement that require the ... 20090298059 - System for the integrated and automated analysis of dna or protein and method for operating said type of system - An embodiment of the present invention relates to a system for the integrated and automated analysis of DNA or protein, including a single-use cartridge, an analysis device comprising a control device, and devices for capturing and processing signals. An embodiment of the present invention relates, in particular, to the control ... 20090298053 - Use of novel biomarkers for detection of testicular carcinoma in situ and derived cancers in human samples - The present invention relates to methods and kits for identification of testicular carcinoma in situ (CIS), gonadoblastoma (a CIS-like pre-cancerous lesion found in dysgenetic gonads) and CIS-derived cancers based on at least one of the biomarkers included in the invention. It also relates to diagnosis of a subject's status of ... ###  How KEYWORD MONITOR works... a FREE service from FreshPatents1. Sign up (takes 30 seconds). 2. Fill in the keywords to be monitored. 3. Each week you receive an email with patent applications related to your keywords. Start now! - Receive info on patent apps like Methods for identifying functionally related genes and drug targets or other areas of interest. ### Previous Patent Application: Methods for identification of bioagents Next Patent Application: Methods of identifying point mutations in a genome that affect the risk for or the age of appearance of disease Industry Class: Chemistry: molecular biology and microbiology ### FreshPatents.com Support Thank you for viewing the Methods for identifying functionally related genes and drug targets patent info. IP-related news and info Results in 2.56713 seconds Other interesting Feshpatents.com categories: Novartis , Pfizer , Philips , Polaroid , Procter & Gamble , paws |
 * Protect your Inventions * US Patent Office filing 
PATENT INFO |
|
