Other

University of California

Ludwig Institute for Cancer Research Limited

Sidney Kimmel Cancer Center

Daniel Mercola

Eileen Adamson

Ian De Belle

Michael McClelland

Robert Oden Stuart

William Wachsman

Steven Goodison

David Tarin

Igor Klacansky

Charles C Berry

Karen Arden

Jessica Wang-Rodriguez

Linda Wasserman

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.

Cell-type-specific patterns of gene expression

The present invention provides methods and compositions for isolating a nucleic acid molecule fragment comprising at least a portion of a gene, comprising: stimulating at least one cell or at least one nucleus with radiation; cross-linking at least one transcription factor to a nucleic acid molecule in said at least one cell or at least one nucleus with formaldehyde, forming at least one transcription factor-nucleic acid molecule complex; fragmenting said nucleic acid molecule to form at least one transcription factor-nucleic acid molecule fragment complex; and isolating the nucleic acid molecule fragment from said at least one transcription factor-nucleic acid molecule fragment complex to form at least one isolated nucleic acid molecule fragment; wherein said at least one isolated nucleic acid molecule fragment comprises at least a portion of the first exon of a gene whose expression is modulated by said transcription factor; further wherein said at least one isolated nucleic acid molecule fragment comprises at least one transcription factor binding site that is operably linked or in close proximity to said first exon of a gene.

Isolation and identification of control sequences and genes modulated by transcription factors

The present invention provides compositions that can be administered to an individual and inhibit a stress activated protein kinase pathway. The invention also provides methods of increasing the sensitivity of cancer cells to a cancer therapy by contacting the cancer cells with a stress activated protein kinase pathway inhibitor. The invention further provides methods of reducing the severity of a cancer in a patient by administering to the patient a stress activated protein kinase pathway inhibitor and treating the patient with a conventional cancer therapy.

Inhibition of stress activated protein kinase (SAPK) pathway and sensitization of cells to cancer therapies

The present invention provides methods for the identification of nucleic acid molecules corresponding to genes regulated by a transcription factor comprising: cross-linking a transcription factor to a nucleic acid molecule in a cell forming a transcription factor-nucleic acid molecule complex; fragmenting the nucleic acid molecule to form a transcription factor-nucleic acid molecule fragment complex; isolating the nucleic acid molecule fragment; combining the isolated nucleic acid molecule fragment with a cDNA library of sequences known to be complementary to previously identified nucleic acid molecules, or a cDNA obtained by reverse transcription of a population of RNA molecules, to form a mixture comprising an isolated nucleic acid molecule fragment-cDNA complex; amplifying the cDNA in the isolated nucleic acid fragment-cDNA complex using the nucleic acid molecule fragment as a primer; and identifying the amplified cDNA molecule by sequencing the cDNA molecule and comparing to known sequences or hybridization to known sequences.

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Rancho Santa Fe, CA, United States of America

Daniel Mercola