Patents Assigned to Expression Pathology, Inc.
-
Patent number: 10725051Abstract: The current disclosure provides specific peptides, and derived ionization characteristics of the peptides from the estrogen receptor (ER), progesterone receptor (PR), and/or antigen Ki67 (Ki67) proteins that are particularly advantageous for quantifying the ER, PR, and/or Ki67 proteins directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring/Multiple Reaction Monitoring (SRM/MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein 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: GrantFiled: October 15, 2018Date of Patent: July 28, 2020Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Todd Hembrough, Sheeno Thyparambil, Wei-Li Liao
-
Patent number: 10718780Abstract: The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the tyrosine-protein kinase receptor UFO protein (AXL) that are particularly advantageous for quantifying the AXL 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: February 12, 2019Date of Patent: July 21, 2020Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Todd Hembrough, Adele Blackler, Wei-Li Liao
-
Patent number: 10620223Abstract: Methods are provided for quantifying the fibroblast growth factor receptor 2 protein (FGFR2) directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM)/Multiple Reaction Monitoring (MRM) mass spectrometry. The biological sample may be 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. A protein sample is prepared from the biological sample and the FGFR2 protein is quantitated in the sample using the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one fragment peptide derived from FGFR2.Type: GrantFiled: May 16, 2016Date of Patent: April 14, 2020Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Todd Hembrough, Sheeno Thyparambil, Wei-Li Liao
-
Methods of treating lung cancer by predicting responders to cisplatin-pemetrexed combination therapy
Patent number: 10617717Abstract: Methods are provided for identifying whether a lung tumor will be responsive to treatment with the combination of the therapeutic agents cisplatin and pemetrexed. Specified ERCC1, TS, p16, and FR? fragment peptides are precisely detected and quantitated by SRM-mass spectrometry directly in lung tumor cells collected from lung tumor tissue that was obtained from a cancer patient and compared to reference levels in order to determine if the lung cancer patient will positively respond to treatment with the combination of cisplatin and pemetrexed therapeutic agents.Type: GrantFiled: December 4, 2017Date of Patent: April 14, 2020Assignee: Expression Pathology, Inc.Inventors: Todd Hembrough, Fabiola Cecchi, Jean-Charles Soria -
Patent number: 10585099Abstract: Methods are provided for quantifying specific proteins directly in biological samples that have been fixed in formalin by SRM/MRM assay. 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. A protein digest is prepared from the biological sample using, for example, the Liquid Tissue reagents and protocol and a designated protein is quantitated in the digest sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the described peptides. The proteins that can be detected and/or quantitated are CD3D, B7H3, B7-2, STAT1, GBP1, GPNMB, CD27, CD3E, and CD8.Type: GrantFiled: November 13, 2017Date of Patent: March 10, 2020Assignee: EXPRESSION PATHOLOGY, INC.Inventors: Todd Hembrough, Fabiola Cecchi, Sarit Schwartz, Kerry Scott
-
Patent number: 10577641Abstract: 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: GrantFiled: September 18, 2017Date of Patent: March 3, 2020Assignee: EXPRESSION PATHOLOGY, INC.Inventor: David Krizman
-
Patent number: 10537576Abstract: Methods of treating breast cancer are provided where a quantitative Her2 assay is used to identify whether a breast tumor will be responsive to treatment with anti-Her2 therapeutic agents such as lapatinib and trastuzumab, followed by selection of a suitable treatment regimen and administration of the regimen. A specific Her2 fragment peptide is precisely quantitated by SRM-mass spectrometry directly in breast tumor cells collected from breast tumor tissue that was obtained from a cancer patient and compared to a reference level in order to determine if the breast cancer patient will positively respond to treatment with a therapeutic agent that specifically targets the Her2 protein.Type: GrantFiled: December 9, 2016Date of Patent: January 21, 2020Assignee: Expression Pathology, Inc.Inventors: Adele Blackler, Todd Hembrough, Fabiola Cecchi, Paolo Nuciforo
-
Publication number: 20190368986Abstract: The current invention provides a method for directly converting histopathologically processed biological samples, tissues, and cells into a multiuse 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: ApplicationFiled: August 14, 2019Publication date: December 5, 2019Applicant: Expression Pathology, Inc.Inventors: Marlene M. DARFLER, David B. KRIZMAN
-
Patent number: 10444126Abstract: Methods are provided for directly converting histopathologically processed biological samples, tissues, and cells into a multiuse 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 biochemical assays.Type: GrantFiled: September 29, 2015Date of Patent: October 15, 2019Assignee: EXPRESSION PATHOLOGY, INC.Inventors: Marlene M. Darfler, David B. Krizman
-
Publication number: 20190293652Abstract: Methods are provided for identifying whether a tumor will be responsive to treatment with an anti-EGFR agent. Specific protein fragment peptides are precisely detected and quantitated by SRM-mass spectrometry directly in tumor cells collected from tumor tissue that was obtained from a cancer patient and compared to reference levels in order to determine if the lung cancer patient will positively respond to treatment with an anti-EGFR agent such as, for example, pamitumumab and/or erbitux.Type: ApplicationFiled: January 20, 2017Publication date: September 26, 2019Applicants: Expression Pathology, Inc., NantOmics, LLCInventors: Fabiola CECCHI, Adele BLACKLER, Wei-Li LIAO, Todd HEMBROUGH, Daniel CATENACCI
-
Patent number: 10302656Abstract: 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: GrantFiled: May 16, 2016Date of Patent: May 28, 2019Assignee: Expression Pathology, Inc.Inventors: David Krizman, Todd Hembrough, Sheeno Thyparambil
-
Patent number: 10288616Abstract: Methods are provided for treating a gastric cancer patient. A specific Met fragment peptide is precisely quantitated by SRM-mass spectrometry directly in gastric tumor cells collected from gastric tumor tissue that was obtained from the cancer patient and compared to a reference level. If the Met peptide is below the reference level a second therapeutic regimen is used to treat the patient whereas if the Met peptide is above the reference level then a first therapeutic regimen combining, for example, the second regimen with one or more Met inhibitor therapeutic agents may be used to treat the patient.Type: GrantFiled: September 26, 2016Date of Patent: May 14, 2019Assignees: Expression Pathology, Inc., The University Of ChicagoInventors: Daniel Catenacci, Todd Hembrough, Fabiola Cecchi, Wei-Li Liao
-
Patent number: 10215761Abstract: 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: GrantFiled: September 12, 2016Date of Patent: February 26, 2019Assignee: Expression Pathology, Inc.Inventors: David Krizman, Todd Hembrough, Sheeno Thyparambil, Wei-Li Liao
-
Patent number: 10208130Abstract: Improved methods of treatment are provided for patients suffering from cancer. The methods identify whether a tumor will be responsive to treatment with a therapeutic regime that includes anti-Her2 therapeutic agents. A specific Her2 fragment peptide is precisely quantitated by SRM-mass spectrometry directly in tumor cells collected from tumor tissue that was obtained from a cancer patient and compared to a reference level in order to determine if the cancer patient will positively respond to treatment with a therapeutic agent that specifically targets the Her2 protein.Type: GrantFiled: May 31, 2016Date of Patent: February 19, 2019Assignees: Expression Pathology, Inc., Department of Internal Medicine and Cancer Research, Seoul National University HospitalInventors: Yung-Jue Bang, Todd Hembrough, Eunkyung An, Do-Youn Oh
-
Patent number: 10203336Abstract: Peptides from the tyrosine-protein kinase receptor UFO protein (AXL) are provided that are particularly advantageous for quantifying the AXL protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM)/Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed and include formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks. A protein digest is prepared from the biological sample and the AXL protein is quantitated in the Liquid Tissue sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described.Type: GrantFiled: April 30, 2015Date of Patent: February 12, 2019Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Todd Hembrough, Adele Blackler, Wei-Li Liao
-
Patent number: 10202635Abstract: Specific peptides, and derived ionization characteristics of the peptides, from the Ephrin Type-A Receptor 2 (EPHA2) protein are provided that are particularly advantageous for quantifying the EPHA2 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 and are 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: April 4, 2014Date of Patent: February 12, 2019Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Wei-Li Liao, Sheeno Thyparambil, Todd Hembrough
-
Patent number: 10126307Abstract: Methods are provided for quantifying the Androgen receptor protein (AR) protein directly in biological samples that have been fixed in formalin, using Selected Reaction Monitoring (SRM)/Multiple Reaction Monitoring (MRM) mass spectrometry. The biological samples are chemically preserved and fixed and can be, for example, tissues 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. A protein sample is prepared from said biological sample using, for example, the Liquid Tissue protocol and the AR protein is quantitated in the Liquid Tissue sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described.Type: GrantFiled: April 30, 2015Date of Patent: November 13, 2018Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Todd Hembrough, Sheeno Thyparambil, Eunkyung An
-
Patent number: 10101334Abstract: The current disclosure provides specific peptides, and derived ionization characteristics of the peptides from the estrogen receptor (ER), progesterone receptor (PR), and/or antigen Ki67 (Ki67) proteins that are particularly advantageous for quantifying the ER, PR, and/or Ki67 proteins directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring/Multiple Reaction Monitoring (SRM/MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein 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: GrantFiled: June 6, 2016Date of Patent: October 16, 2018Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Todd Hembrough, Sheeno Thyparambil, Wei-Li Liao
-
Patent number: 10078084Abstract: Methods are provided for detecting and quantifying the Mesothelin protein (MSLN) in biological samples that have been fixed in formalin using Selected Reaction Monitoring (SRM)/Multiple Reaction Monitoring (MRM) mass spectrometry. The biological sample may be, for example, 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. A protein sample is prepared from the biological sample and the MSLN protein is quantitated by SRM/MRM mass spectrometry by quantitating one or more MSLN fragment peptides in the protein sample.Type: GrantFiled: May 16, 2016Date of Patent: September 18, 2018Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Todd Hembrough, Eunkyung An, Sheeno Thyparambil
-
Patent number: 10073075Abstract: Methods are provided for quantifying the cyclin-dependent kinase inhibitor 2A protein (p16) p16 protein directly in biological samples that have been fixed in formalin by SRM/MRM mass spectrometry. A protein sample is prepared from the biological sample using, for example, the Liquid Tissue reagents and protocol and the p16 protein is quantitated in the resulting sample by quantitating in the protein sample at least one fragment peptide from p16. Peptides can be quantitated in modified or unmodified form. An example of a modified form of a p16 peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.Type: GrantFiled: May 23, 2016Date of Patent: September 11, 2018Assignee: Expression Pathology, Inc.Inventors: David B. Krizman, Todd Hembrough, Eunkyung An