Abstract: Among the methods, compositions, combinations and kits provided herein are those for determining gene expression levels in one or more cell types in heterogeneous cell samples, for identifying genes differentially expressed in different cell types, and for detecting a cell type in a sample from a subject. Also provided herein are methods, compositions, combinations and kits for determining gene expression levels in cells corresponding to phenotypes, and for identifying a phenotype of a subject by detecting differentially expressed genes.

Abstract: The emerging concept of cancer stem cells suggests that activation in transformed cells of “sternness” genetic pathways (e.g., normal stem cells' self-renewal pathways) may contribute to the survival life cycle of cancer stem cells, and to tumor progression and metastasis of the malignancy. Thus, activation of “sternness” genes in cancer cells may be associated with aggressive clinical behavior and increased likelihood of therapy failure. General methods and kits associated with prediction of clinical outcome for a disease state of a subject based on gene expression analysis are described. The invention includes determining expression of at least three genes selected from the group consisting of GBX2, MKI67, CCNB1, BUB1, KNTC2, USP22, HCFC1, RNF2, ANK3, FGFR2, and CES1, and mouse homologs thereof.

Abstract: Methods to prevent the rejection of immunogenic tissues in an animal by administering a non-immunogenic, poorly catabolized molecule in an amount sufficient to inhibit an immune response are described herein. Also described are compositions that are useful for inhibiting immune responses in animals that are recipients of cellular transplants. For example, these methods and compositions can be used to prevent the rejection of xenografted and allografted tissues in an animal.

Abstract: Methods of delivering an agent in a tissue-specific manner, particularly lung tissue, by targeting a protein expressed on the endothelial cell surface, are described. The methods can be used for detecting, imaging and/or treating pathologies, as well as for diagnostics.

Abstract: Methods of delivering an agent in a tissue-specific manner, by targeting annexin A1, a derivative of annexin A1, or a binding partner of annexin A1, are described. The methods can be used for detecting, imaging and/or treating neoplasia, angiogenesis or neovasculature, as well as for diagnostics and methods of assessing treatment efficacy. Antibodies to annexin A1 are also described, as are methods screening for agents altering annexin A1 activity.

Abstract: Methods of delivering an agent in a tissue-specific manner, by targeting proteins expressed on endothelial cell surface, are described. The methods can be used for detecting, imaging and/or treating neoplasia, angiogenesis or neovasculature, as well as for diagnostics and methods of assessing treatment efficacy.

Abstract: General methods of biological sample classification based on gene expression analysis are described. The methods segregate individual samples into distinct classes using quantitative measurements of expression values for selected sets of genes in individual samples compared to a reference standard. Samples displaying positive and negative correlations of the gene expression values with the reference standard samples exhibit distinct behaviors and pathohistological features. Also disclosed are methods for identifying sets of genes whose expression patterns are correlated with a phenotype. Such sets are useful for characterizing cellular differentiation pathways and states and for identifying potential drug discovery targets.

Abstract: General methods of biological sample classification based on gene expression analysis are described. The methods segregate individual samples into distinct classes using quantitative measurements of expression values for selected sets of genes in individual samples compared to a reference standard. Samples displaying positive and negative correlations of the gene expression values with the reference standard samples exhibit distinct behaviors and pathohistological features. Also disclosed are methods for identifying sets of genes whose expression patterns are correlated with a phenotype. Such sets are useful for characterizing cellular differentiation pathways and states and for identifying potential drug discovery targets.

Abstract: The invention provides a method of measuring the level of two or more nucleic acid molecules in a target by contacting a probe with a target comprising two or more nucleic acid molecules, wherein the nucleic acid molecules are arbitrarily sampled and wherein the arbitrarily sampled nucleic acid molecules comprise a subset of the nucleic acid molecules in a population of nucleic acid molecules; and detecting the amount of specific binding of the target to the probe. The invention also provides a method of measuring the level of two or more nucleic acid molecules in a target by contacting a probe with a target comprising two or more nucleic acid molecules, wherein the nucleic acid molecules are statistically sampled and wherein the statistically sampled nucleic acid molecules comprise a subset of the nucleic acid molecules in a population of nucleic acid molecules; and detecting the amount of specific binding of the target to the probe.

Abstract: The invention provides a method of measuring the level of two or more nucleic acid molecules in a target by contacting a probe with a target comprising two or more nucleic acid molecules, wherein the nucleic acid molecules are arbitrarily sampled and wherein the arbitrarily sampled nucleic acid molecules comprise a subset of the nucleic acid molecules in a population of nucleic acid molecules; and detecting the amount of specific binding of the target to the probe. The invention also provides a method of measuring the level of two or more nucleic acid molecules in a target by contacting a probe with a target comprising two or more nucleic acid molecules, wherein the nucleic acid molecules are statistically sampled and wherein the statistically sampled nucleic acid molecules comprise a subset of the nucleic acid molecules in a population of nucleic acid molecules; and detecting the amount of specific binding of the target to the probe.

Abstract: The invention provides a method of preventing or reducing the severity of a cancer in a subject by stimulating the subject's immune response against the cancer. The invention provides, for example, a method of stimulating an immune response in a subject by administering to the subject tumor cells that are substantially similar to the subject's cancer cells and that are genetically modified to reduce or inhibit the expression of one or more immunosuppressive agents. The invention also provides a method of preventing or reducing the severity of cancer in a subject by stimulating the subject's immune response against the cancer by administering to the subject tumor cells that are substantially similar to the subject's cancer cells and that are genetically modified to prevent the expression of an immunosuppressive agents and, in combination with the genetically modified tumor cells, an immunostimulatory agent.

Abstract: The present invention provides an anti-idiotypic antibody having specific reactivity with an idiotope common to more than one type of anti-HIV-1 antibody, and having no specific reactivity with non-HIV-1 antibodies. The present invention provides methods of diagnosis, monitoring and treatment of HIV-related diseases through the use of this antibody or related compounds.

Abstract: The invention provides a method of preventing or reducing the severity of a cancer in a subject by stimulating the subject's immune response against the cancer. The invention provides, for example, a method of stimulating an immune response in a subject by administering to the subject tumor cells that are substantially similar to the subject's cancer cells and that are genetically modified to reduce or inhibit the expression of one or more immunosuppressive agents. The invention also provides a method of preventing or reducing the severity of cancer in a subject by stimulating the subject's immune response against the cancer by administering to the subject tumor cells that are substantially similar to the subject's cancer cells and that are genetically modified to prevent the expression of an immunosuppressive agents and, in combination with the genetically modified tumor cells, an immunostimulatory agent. The invention further provides compositions useful for practicing the claimed methods.

Abstract: The present invention details methods for the treatment of cancer. In particular it concerns the induction of apoptosis in cancer cells following treatment with inhibitors of DNA repair in combination with p53. Treatment of glioblastoma and breast tumor cells with inhibitors of DNA repair induced growth suppression that was a result of p53-mediated apoptosis. Thus it appears that inhibitors of DNA repair in combination with p53 is involved in restoration of p53-mediated apoptosis.

Abstract: The present invention provides an anti-idiotypic antibody having specific reactivity with an idiotope common to more than one type of anti-HIV-1 antibody, and having no specific reactivity with non-HIV-1 antibodies. The present invention provides methods of diagnosis, monitoring and treatment of HIV-related diseases through the use of this antibody or related compounds.

Abstract: The invention provides a method of preventing or reducing the severity of a cancer in a subject by stimulating the subject's immune response against the cancer. The invention provides, for example, a method of stimulating an immune response in a subject by administering to the subject tumor cells that are substantially similar to the subject's cancer cells and that are genetically modified to reduce or inhibit the expression of one or more immunosuppressive agents. The invention also provides a method of preventing or reducing the severity of cancer in a subject by stimulating the subject's immune response against the cancer by administering to the subject tumor cells that are substantially similar to the subject's cancer cells and that are genetically modified to prevent the expression of an immunosuppressive agents and, in combination with the genetically modified tumor cells, an immunostimulatory agent. The invention further provides compositions useful for practicing the claimed methods.

Abstract: A novel method of tumor immunotherapy is described comprising the genetic modification of cells resulting in the secretion of cytokine gene products to stimulate a patient's immune response to tumor antigens. In one embodiment, autologous fibroblasts genetically modified to secrete at least one cytokine gene product are utilized to immunize the patient in a formulation with tumor antigens at a site other than an active tumor site. In another embodiment, cells genetically modified to express at least one tumor antigen gene product and to secrete at least one cytokine gene product are utilized in a formulation to immunize the patient at a site other than an active tumor site.