# US 2014/0193835 A1 · Cell-based detection of apf through its interaction with ckap4 for diagnosis of interstitial cystitis > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2014/0193835 A1 - Document ID: US20140193835A1 - Status: Published application - Kind: A1 - Application number: 13/911,242 - Filed: 2013-06-06 - Published: 2014-07-10 - Earliest claimed: 2008-12-12 - Assignees: University of Florida Research Foundation, Inc.; The Commonwealth Medical College - Applicants: University of Florida Research Foundation, Inc.; The Commonwealth Medical College - Inventors: David Alan ZACHARIAS; Sonia Lobo PLANEY - Web page: https://patentgrep.com/patent/US20140193835A1 ## CPC - G01N 33/5091: {for testing the pathological state of an organism} - C07K 9/005: {containing within the molecule the substructure [IMAGE cpc-sch-C07K-1009.gif] with m, n > 0 and m+n > 0, A, B, D, E being heteroatoms; X being a bond or a chain, e.g. muramylpeptides} - C07K 14/705: Receptors; Cell surface antigens; Cell surface determinants {(tumour specific antigens C07K14/4748)} - C12Q 1/6897: involving reporter genes operably linked to promoters - G01N 33/6893: {related to diseases not provided for elsewhere} - G01N 2333/4728: alpha-Glycoproteins - G01N 2800/34: Genitourinary disorders - Y10T 436/110833: Utilizing a moving indicator strip or tape - Y10T 436/112499: with sample on test slide - 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) - C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00) - 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 - Y10T: TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION ## Abstract An assay system designed to detect a protein biomarker in urine that is diagnostic for interstitial cystitis (IC). The presence of a 9 amino acid glycopeptide, antiproliferative factor (APF), in urine is unique to patients with IC. Urine samples from patients who exhibit symptoms consistent with IC are added to the assay system. Binding of APF to the cytoskeletal associated protein 4 (CKAP4) is positive for the presence of APF in urine and diagnostic for IC. The diagnostic system is a significant and surprising advance in diagnosis of IC and has commercial applications relevant to women and men who suffer from symptoms consistent with IC. ## Claims ### Claim 1 A method for diagnosis of interstitial cystitis in a patient by detecting the presence of APF in a biological sample comprising: (a) providing a detectably labeled first CKAP4 protein, fragments thereof, and variants thereof, wherein the CKAP4 protein is capable of binding APF; (b) providing a detectably labeled second CKAP4 protein, fragments thereof, and variants thereof, wherein the CKAP4 protein is capable of binding APF; (c) providing a biological sample from a patient; (d) contacting the detectably labeled first CKAP4 protein with the biological sample to provide a first test sample; (e) providing a control sample; (f) contacting the detectably labeled second CKAP4 protein with the control sample to provide a second test sample; (g) measuring the label in the first test sample; (h) measuring the label in the second test sample; and (i) assessing the label in the first test sample relative to the label in the second test sample, wherein detecting an increase in the first test sample identifies the presence of APF in the biological sample, thereby indicating IC disease. ### Claim 2 (depends on 1) The method of claim 1, wherein the method of measurement is selected from the group consisting of fluorescence resonance electron transfer (FRET), lanthanide resonance electron transfer (LRET), fluorescence cross-correlation spectroscopy, fluorescence quenching, fluorescence polarization, flow cytometry, scintillation proximity, luminescence resonance energy transfer, direct quenching, ground-state complex formation, chemiluminescence energy transfer, bioluminescence resonance energy transfer, excimer formation, colorimetric substrates detection, phosphorescence, electro-chemical changes, and redox potential changes. ### Claim 3 (depends on 1) The method of claim 1, wherein the method of measurement is generated/detected following APF binding due to a change in the conformation of the receptor, a change in protein-protein interactions, a change in membrane-protein interactions or other, the other interacting partners being labeled with an appropriate fluorophore to serve as a resonance energy donor or acceptor that appropriately complements the donor or acceptor fluorophore that is attached to CKAP4. ### Claim 4 (depends on 1) The method of claim 1, wherein the signals from FRET, BRET, LRET and LET may be detected either intramolecularly, where the donor and acceptor fluorophore are part of the same sensor molecule or intermolecularly where the donor and acceptor are physically associated with two separate molecules, one of which may be CKAP4, the other any molecule that interacts with CKAP4 in an APF-dependent manner. ### Claim 5 A kit for detecting interstitial cystitis in a patient by detecting the presence of APF in a biological sample, said kit comprising: (a) at least one detection reagent which is selected from the group consisting of a detectably labeled CKAP4 protein, fragments thereof, and variants thereof, wherein the CKAP4 protein is capable of binding APF; wherein said at least one detection reagent is adapted to detect a threshold level of said APF, said threshold level adapted to indicate a presence of interstitial cystitis; and (b) instructions for using said at least one detection reagent to evaluate interstitial cystitis in the patient. ### Claim 6 (depends on 5) A kit according to claim 5, wherein the biological sample is urine. ### Claim 7 (depends on 5) A kit according to claim 5, wherein said kit comprises a detector device. ### Claim 8 (depends on 5) A kit according to claim 5, wherein said kit comprises a dipstick, a swab, and a container. ### Claim 9 (depends on 5) A kit of claim 5, wherein the detection reagents are attached to a detectable label. ### Claim 10 (depends on 5) A kit of claim 5, further comprising one or both of a positive and a negative control. ### Claim 11 (depends on 7) A kit according to claim 7, wherein said detector device is a dipstick. ### Claim 12 (depends on 7) A kit according to claim 7, wherein the detector device comprises a housing having a chamber consisting of one or more test wells disposed inside the housing and having an inlet above each well to allow the introduction of a biological samples, wherein each test well may contain a detection reagent. ### Claim 13 (depends on 7) A kit according to claim 7, wherein the detector device housing may be at least partially transparent, or has windows provided therein, for observation of an indicator region that undergoes a color or fluorescence change. ### Claim 14 (depends on 7) A kit according to claim 7, wherein the detector device is selected from the group consisting of a dipstick, a lateral flow device, and migration-type device. ### Claim 15 (depends on 14) A kit according to claim 14, wherein the detector device is a lateral flow device comprising a housing having an inlet for the sample and side walls defining a fluid lateral flow path extending from the inlet.