# US 2024/0201190 A1 · Compositions and methods of diagnosing pancreatic cancer > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2024/0201190 A1 - Document ID: US20240201190A1 - Status: Published application - Kind: A1 - Application number: 18/350,009 - Filed: 2023-07-11 - Published: 2024-06-20 - Earliest claimed: 2017-04-03 - Assignees: The Regents of the University of California - Applicants: The Regents of the University of California - Inventors: Sam L. IVRY; Anthony J. O'DONOGHUE; Kimberly KIRKWOOD; Charles S. CRAIK - Web page: https://patentgrep.com/patent/US20240201190A1 ## CPC - G01N 33/57525: of the liver or pancreas - C12N 9/6478: {Aspartic endopeptidases (3.4.23)} - C12Q 1/37: involving peptidase or proteinase - G01N 33/6848: {Methods of protein analysis involving mass spectrometry} - G01N 33/57565: {involving carcinoembryonic antigen [CEA]} - G01N 2333/96416: Aspartic endopeptidases (3.4.23) - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract The present disclosure relates generally to detection of molecular biomarkers in a sample or diagnosis of a subject based upon detection or quantification of molecular biomarkers in a sample, specifically to the identification and use of biomarkers for pancreatic cysts. ## Claims ### Claim at position 1 1-59. (canceled) ### Claim 60 A method of determining whether a subject has a mucinous cyst or malignant growth comprising detecting the presence, absence, or quantity of CEA in a sample of the subject, wherein the sensitivity to detecting CEA is equal to or greater than 70%. ### Claim at position 3 -75. (canceled) ### Claim 76 (depends on 60) The method of claim 60, wherein the step of detecting comprises detecting the quantity of CEA in a sample from the subject. ### Claim 77 (depends on 76) The method of claim 76, wherein the sample is a sample of cystic fluid. ### Claim 78 (depends on 60) The method of claim 60 further comprising (a) contacting a one or a plurality of probes specific for CEA and/or functional fragments thereof with a sample from the subject; (b) quantifying the amount of CEA and/or functional fragment thereof in the sample; (c) calculating one or more normalized scores based upon the presence, absence, or quantity of CEA and/or functional fragment thereof; and (d) correlating the one or more scores to the presence, absence, or quantity of CEA and/or functional fragment thereof, such that if the amount of CEA and/or functional fragment thereof is greater than the quantity of CEA and/or functional fragment thereof in a control sample, the correlating step comprises characterizing the sample as comprising a mucinous cyst or malignant growth. ### Claim 79 (depends on 78) The method of claim 78 further comprising (a) contacting a one or a plurality of probes specific for cathepsin E and/or functional fragments thereof with a sample from the subject; (b) quantifying the amount of cathepsin E and/or functional fragment thereof in the sample; (c) calculating one or more normalized scores based upon the presence, absence, or quantity of cathepsin E and/or functional fragment thereof; and (d) correlating the one or more scores to the presence, absence, or quantity of cathepsin E and/or functional fragment thereof, such that if the amount of cathepsin E and/or functional fragment thereof is greater than the quantity of cathepsin E and/or functional fragment thereof in a control sample, the correlating step comprises characterizing the sample as comprising a pre-cancerous or cancerous cell. ### Claim 80 (depends on 78) The method of claim 78 further comprising: (a) contacting a one or a plurality of probes specific for gastricsin and/or functional fragments thereof with a sample from the subject; (b) quantifying the amount of gastricsin and/or functional fragment thereof in the sample; (c) calculating one or more normalized scores based upon the presence, absence, or quantity of gastricsin and/or functional fragment thereof; and (d) correlating the one or more scores to the presence, absence, or quantity of gastricsin and/or functional fragment thereof, such that if the amount of gastricsin and/or functional fragment thereof is greater than the quantity of gastricsin and/or functional fragment thereof in a control sample, the correlating step comprises characterizing the sample as comprising a pre-cancerous or cancerous cell. ### Claim 81 (depends on 60) The method of claim 60 further comprising detecting the presence, absence, and/or quantity of at least one aspartyl protease or functional fragment thereof in the sample. ### Claim 82 (depends on 81) The method of claim 81, wherein the step of detecting the presence, absence, and/or quantity of at least one aspartyl protease or functional fragment thereof comprises exposing the sample to at least one substrate of an aspartyl protease or functional fragment thereof or at least one molecule capable of reacting with or binding to at least one aspartyl protease or functional fragment thereof. ### Claim 83 (depends on 82) The method of claim 82, wherein the step of detecting the presence, absence, and/or quantity of at least one aspartyl protease or functional fragment thereof further comprises measuring the quantity of the at least one aspartyl protease or functional fragment thereof in the sample by one or a combination of: (i) digitally imaging the sample; (ii) exposing the sample to a known amount of labeled antibody specific for an epitope of the at least one aspartyl protease, or a functional fragment thereof; (iii) exposing the sample to a library of substrates the at least one aspartyl protease or functional fragment thereof; (iv) exposing the sample to at least one labeled antibody specific for an epitope of the at least one aspartyl protease or functional fragment thereof; (v) exposing the sample to chromatography; and/or (vi) exposing the sample to mass spectrometry. ### Claim 84 (depends on 83) The method of claim 83, wherein the at least one aspartyl protease or functional fragment thereof is gastricsin, cathepsin E, or a functional fragment thereof. ### Claim 85 (depends on 81) The method of claim 81, wherein detecting the presence, absence, and/or quantity of at least one aspartyl protease or functional fragment thereof comprises: (i) contacting the sample to at least one substrate specific for cathepsin E, gastricsin, functional fragments thereof, or combinations thereof; and (ii) calculating one or more scores based upon the presence, absence, or quantity of cathepsin E and/or gastricsin and/or functional fragment thereof. ### Claim 86 (depends on 85) The method of claim 85 wherein detecting the presence, absence, and/or quantity of at least one aspartyl protease or functional fragment thereof further comprises: (iii )correlating the one or more scores to the presence, absence, or quantity of cathepsin E and/or gastricsin and/or functional fragment thereof, such that, if the amount of cathepsin E and/or gastricsin and/or functional fragment thereof is greater than the quantity of cathepsin E and/or gastricsin and/or functional fragment thereof in a control sample; or, if the amount of cathepsin E and/or gastricsin and/or functional fragment thereof is substantially equal to or greater than the quantity of cathepsin E and/or gastricsin and/or functional fragment thereof in a sample taken from a subject known to have a mucinous cyst, then the subject has a mucinous cyst or malignant growth. ### Claim 87 (depends on 85) The method of claim 85, wherein the substrate specific for cathepsin E, gastricsin, or functional fragments thereof is one or a plurality of substrates chosen from a substrate having an amino acid sequence with formula: DEGWALQH (SEQ ID NO: 1), VGKWSYRM (SEQ ID NO: 2), NMKWTRVL (SEQ ID NO: 3), PWTWYGVK (SEQ ID NO: 4), FGIFYLNG (SEQ ID NO: 5), HMIALYWG (SEQ ID NO: 6), IKILMFYW (SEQ ID NO: 7), GLYFRYE (SEQ ID NO: 8), AGFSLPA (SEQ ID NO: 9), or an analog that is at least 70% homologous to the amino acid sequences SEQ ID NO: 1 through SEQ ID NO:9. ### Claim 88 (depends on 85) The method of claim 85, wherein the substrate specific for cathepsin E, gastricsin, or functional fragments thereof is an amino acid comprising at least 87% homology to one or a plurality of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, and SEQ ID NO:9.