Patents Assigned to Expression Pathology, Inc.
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Publication number: 20150369818Abstract: The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the Receptor Tyrosine-Protein Kinase erbB-3, or Her3, that are particularly advantageous for quantifying the Her3 protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein said biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded.Type: ApplicationFiled: September 8, 2015Publication date: December 24, 2015Applicant: Expression Pathology, Inc.Inventors: David KRIZMAN, Todd Hembrough, Sheeno Thyparambil
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Liquid tissue preparation from histopathologically processed biologically samples, tissues and cells
Patent number: 9163275Abstract: The current invention provides a method for directly converting histopathologically processed biological samples, tissues, and cells into a multi-use biomolecule lysate. This method allows for simultaneous extraction, isolation, solublization, and storage of all biomolecules contained within the histopathologically processed biological sample, thereby forming a representative library of said sample. This multi-use biomolecule lysate is dilutable, soluble, capable of being fractionated, and used in any number of subsequent experiments.Type: GrantFiled: May 17, 2013Date of Patent: October 20, 2015Assignee: EXPRESSION PATHOLOGY, INC.Inventors: Marlene M. Darfler, David B. Krizman -
Patent number: 9139864Abstract: Objective quantitation of the c-Src protein directly in cancer patient tissue can aid in determining the aggressiveness of an individual patient's tumor as well as help make more informed decisions about choice of therapy. However, the c-Src protein is currently analyzed directly in formalin fixed patient tissue only by immunohistochemistry methodology which is at best subjectively semi-quantitative. This invention describes an objective quantitative assay for the c-Src protein using mass spectrometry as the analytical methodology. Specific peptides, experimentally discovered characteristics about the peptides, and experimentally established assay conditions based on those peptide characteristics are provided for use in a mass spectrometry-based Selected Reaction Monitoring (SRM) assay in order to measure relative or absolute quantitative levels of c-Src directly in a protein preparation obtained from a formalin fixed cancer patient tissue sample.Type: GrantFiled: January 30, 2013Date of Patent: September 22, 2015Assignee: EXPRESSION PATHOLOGY, INC.Inventor: David B. Krizman
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Patent number: 9128102Abstract: The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the Receptor Tyrosine-Protein Kinase erbB-3, or Her3, that are particularly advantageous for quantifying the Her3 protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein said biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded.Type: GrantFiled: July 1, 2013Date of Patent: September 8, 2015Assignee: EXPRESSION PATHOLOGY, INC.Inventors: David Krizman, Todd Hembrough, Sheeno Thyparambil
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Publication number: 20150005183Abstract: This patent application discloses and describes proteins found to be differentially expressed between primary tumor breast cancer cells histologicaly defined as early stage (stage 0) breast cancer and primary breast cancer cells histologicaly defined as late stage (stage 3) breast cancer. These proteins can be used either individually or in specific combinations in diagnostic and prognostic protein assays on various biological samples from breast cancer patients to indicate the that a breast cancer patient's cancer is in an early, non-aggressive stage or in a late, aggressive stage. Determination of differential expression of these proteins can also be useful for indicating additional therapies to combat the aggressiveness of late stage breast cancer. The full length intact proteins can be assayed or peptides derived from these proteins can be assayed as reporters for these proteins.Type: ApplicationFiled: July 1, 2013Publication date: January 1, 2015Applicant: EXPRESSION PATHOLOGY, INC.Inventors: David Krizman, Marlene M. Darfler, Thomas P. Conrads, Brian L. Hood
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Publication number: 20150005182Abstract: This patent application discloses and describes proteins found to be differentially expressed between primary tumor breast cancer cells that did not give rise to recurrent breast cancer disease after initial diagnosis and primary breast cancer cells that did give rise to recurrent breast cancer disease after initial diagnosis. These proteins can be used either individually or in specific combinations in diagnostic and prognostic protein assays on various biological samples from breast cancer patients to indicate the likelihood that a breast cancer patient's cancer will recur after initial diagnosis and treatment. Determination of differential expression of these proteins can also be useful for indicating additional therapies to combat the likelihood of recurrent breast cancer. The full length intact proteins can be assayed or peptides derived from these proteins can be assayed as reporters for these proteins.Type: ApplicationFiled: July 1, 2013Publication date: January 1, 2015Applicant: EXPRESSION PATHOLOGY, INC.Inventors: David Krizman, Marlene M. Darfler, Thomas P. Conrads, Brian L. Hood
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Publication number: 20140005282Abstract: Specific peptides are provided, and derived ionization characteristics of those peptides, from the Hepatocyte Growth Factor Receptor (cMET) protein. The peptides are particularly and surprisingly advantageous for quantifying by the method of Selected Reaction Monitoring (SRM) mass spectrometry the cMET protein directly in biological samples that have been fixed in formalin, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed where the biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including: formalin-fixed tissue/cells; formalin-fixed/paraffin embedded (FFPE) tissue/cells; FFPE tissue blocks and cells from those blocks; and tissue culture cells that have been formalin fixed and or paraffin embedded.Type: ApplicationFiled: December 27, 2011Publication date: January 2, 2014Applicant: EXPRESSION PATHOLOGY, INC.Inventors: David Krizman, Todd Hembrough, Sheeno Thyparambil
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Publication number: 20130302334Abstract: Specific peptides, and derived ionization characteristics of those peptides, from the Bcl-2-like protein 11 (BIM) are provided that are particularly advantageous for quantifying the BIM protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM). Such biological samples are chemically preserved and fixed where the biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded.Type: ApplicationFiled: July 15, 2013Publication date: November 14, 2013Applicant: EXPRESSION PATHOLOGY, INC.Inventors: David Krizman, Todd Hembrough, Sheeno Thyparambil, Wei-Li Liao
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Publication number: 20130302328Abstract: This disclosure provides ten (10) specific peptides, and particular peptide characteristics, from the cell membrane-bound Her2 protein and a diagnostic assay useful for determining the presence and amount of full length and truncated versions of the full-length Her2 protein in cells derived from formalin fixed paraffin embedded tissue.Type: ApplicationFiled: December 8, 2011Publication date: November 14, 2013Applicant: Expression Pathology, Inc.Inventor: David Krizman
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Publication number: 20130289142Abstract: The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the Receptor Tyrosine-Protein Kinase erbB-3, or Her3, that are particularly advantageous for quantifying the Her3 protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein said biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded.Type: ApplicationFiled: July 1, 2013Publication date: October 31, 2013Applicant: EXPRESSION PATHOLOGY, INC.Inventors: David Krizman, Todd Hembrough, Sheeno Thyparambil
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LIQUID TISSUE PREPARATION FROM HISTOPATHOLOGICALLY PROCESSED BIOLOGICALLY SAMPLES, TISSUES AND CELLS
Publication number: 20130252840Abstract: The current invention provides a method for directly converting histopathologically processed biological samples, tissues, and cells into a multi-use biomolecule lysate. This method allows for simultaneous extraction, isolation, solublization, and storage of all biomolecules contained within the histopathologically processed biological sample, thereby forming a representative library of said sample. This multi-use biomolecule lysate is dilutable, soluble, capable of being fractionated, and used in any number of subsequent experiments.Type: ApplicationFiled: May 17, 2013Publication date: September 26, 2013Applicant: Expression Pathology, Inc.Inventors: Marlene M. Darfler, David B. Krizman -
Patent number: 8455215Abstract: The current invention provides a method for directly converting histopathologically processed biological samples, tissues, and cells into a multi-use biomolecule lysate. This method allows for simultaneous extraction, isolation, solubilization, and storage of all biomolecules contained within the histopathologically processed biological sample, thereby forming a representative library of said sample. This multi-use biomolecule lysate is dilutable, soluble, capable of being fractionated, and used in any number of subsequent experiments.Type: GrantFiled: January 5, 2009Date of Patent: June 4, 2013Assignee: Expression Pathology, Inc.Inventors: Marlene M. Darfler, David B. Krizman
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Publication number: 20130131195Abstract: Objective quantitation of the c-Src protein directly in cancer patient tissue can aid in determining the aggressiveness of an individual patient's tumor as well as help make more informed decisions about choice of therapy. However, the c-Src protein is currently analyzed directly in formalin fixed patient tissue only by immunohistochemistry methodology which is at best subjectively semi-quantitative. This invention describes an objective quantitative assay for the c-Src protein using mass spectrometry as the analytical methodology. Specific peptides, experimentally discovered characteristics about the peptides, and experimentally established assay conditions based on those peptide characteristics are provided for use in a mass spectrometry-based Selected Reaction Monitoring (SRM) assay in order to measure relative or absolute quantitative levels of c-Src directly in a protein preparation obtained from a formalin fixed cancer patient tissue sample.Type: ApplicationFiled: January 30, 2013Publication date: May 23, 2013Applicant: EXPRESSION PATHOLOGY, INC.Inventor: Expression Pathology, Inc.
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Publication number: 20130079425Abstract: Specific peptides are provided that are derived from subsequences of the urokinase-type plasminogen activator protein and the plasminogen activator inhibitor type-1 protein along with assays that can measure those peptides directly in complex protein lysate samples, including protein lysates prepared from histologicaly-processed formalin fixed tissue. The presence and amount of those peptides in samples from a subject can be associated with disease, including cancer, in a subject and provide information about the diagnostic stage/grade/status of the disease/cancer.Type: ApplicationFiled: November 26, 2012Publication date: March 28, 2013Applicant: EXPRESSION PATHOLOGY, INC.Inventor: Expression Pathology, Inc.
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Publication number: 20130011408Abstract: The current disclosure provides for specific peptides from the Epidermal Growth Factor Receptor (EGFR) protein and the derived ionization characteristics of those peptides that are advantageous for quantifying the EGFR directly in formalin fixed biological samples by the method of Selected Reaction Monitoring (SRM) mass spectrometry. Such fixed biological samples include: formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and formalin fixed and paraffin embedded tissue culture cells. EGFR protein is quantitated in biological samples by the method of SRM/MRM mass spectrometry by quantitating one or more of the peptides described herein. The peptides can be quantitated if they reside in a modified or an unmodified form. Examples of potentially modified forms of an EGFR peptides include those bearing phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.Type: ApplicationFiled: June 21, 2012Publication date: January 10, 2013Applicant: EXPRESSION PATHOLOGY, INC.Inventors: David B. Krizman, Todd Hembrough, Sheeno Thyparambil
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Publication number: 20120302650Abstract: The current disclosure provides for specific peptides from the Insulin-Like Growth Factor 1 Receptor (IGF-1R) protein and the derived ionization characteristics of those peptides that are advantageous for quantifying the IGF-1R directly in formalin fixed biological samples by the method of Selected Reaction Monitoring (SRM) mass spectrometry. Such fixed biological samples include: formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and formalin fixed and paraffin embedded tissue culture cells. IGF-1R protein is quantitated in biological samples by the method of SRM/MRM mass spectrometry by quantitating one or more of the peptides described herein. The peptides can be quantitated if they reside in a modified or an unmodified form. Examples of potentially modified forms of an IGF-1R peptides include those bearing phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.Type: ApplicationFiled: June 21, 2012Publication date: November 29, 2012Applicant: EXPRESSION PATHOLOGY, INC.Inventors: David B. Krizman, Todd Hembrough, Sheeno Thyparambil
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Publication number: 20120295990Abstract: The current disclosure provides for specific peptides from the Insulin Receptor Substrate 1 (IRS1) protein and the derived ionization characteristics of those peptides that are advantageous for quantifying IRS1 directly in formalin fixed biological samples by the method of Selected Reaction Monitoring (SRM) mass spectrometry. Such fixed biological samples include: formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and formalin fixed and paraffin embedded tissue culture cells. IRS1 protein is quantitated in biological samples by the method of SRM/MRM mass spectrometry by quantitating one or more of the peptides described herein. The peptides can be quantitated if they reside in a modified or an unmodified form. Examples of potentially modified forms of IRS1 peptides include those bearing phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.Type: ApplicationFiled: June 21, 2012Publication date: November 22, 2012Applicant: EXPRESSION PATHOLOGY, INCInventors: David B. KRIZMAN, Todd Hembrough, Sheeno Thyparambil
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Patent number: 8293485Abstract: The invention provides methods for multiplex analysis of biological samples of formalin-fixed tissue samples. The invention provides for a method to achieve a multiplexed, multi-staged plurality of Liquid Tissue preparations simultaneously from a single histopathologically processed biological sample, where the protocol for each Liquid Tissue preparation imparts a distinctive set of biochemical effects on biomolecules procured from histopathologically processed biological samples and which when each of the preparations is analyzed can render additive and complementary data about the same histopathologically processed biological sample.Type: GrantFiled: March 15, 2011Date of Patent: October 23, 2012Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Marlene M. Darfler
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Patent number: 7906301Abstract: The invention provides methods for multiplex analysis of biological samples of formalin-fixed tissue samples. The invention provides for a method to achieve a multiplexed, multi-staged plurality of Liquid Tissue preparations simultaneously from a single histopathologically processed biological sample, where the protocol for each Liquid Tissue preparation imparts a distinctive set of biochemical effects on biomolecules procured from histopathologically processed biological samples and which when each of the preparations is analyzed can render additive and complementary data about the same histopathologically processed biological sample.Type: GrantFiled: May 25, 2006Date of Patent: March 15, 2011Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Marlene M. Darfler
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Publication number: 20110028344Abstract: This patent application discloses and describes a list of proteins that are found to be differentially expressed between normal endometrial epithelial cells and early stage cancerous endometrial epithelial cells. These proteins can be used either individually or in specific combinations in diagnostic and prognostic protein assays on various biological samples from endometrial cancer patients, or individuals suspected on having endometrial cancer. In addition, these proteins are also differentially expressed between normal endometrial epithelial cells and epithelial cells of other types of endometrial disease, and thus such diseases can be diagnosed using assays based on these proteins. The full length intact proteins can be assayed or peptides derived from these proteins can be assayed as reporters for these proteins.Type: ApplicationFiled: April 13, 2009Publication date: February 3, 2011Applicant: Expression Pathology, Inc.Inventors: David B. Krizman, Thomas G. Guiel