(12) Patent Application Publication (10) Pub. No.: US 2014/0228233 A1 Pawlowski Et Al
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US 20140228233A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0228233 A1 Pawlowski et al. (43) Pub. Date: Aug. 14, 2014 (54) CIRCULATING BOMARKERS FOR CANCER Publication Classification (76) Inventors: Traci Pawlowski, Laguna Hills, CA (51) Int. Cl. (US); Kimberly Yeatts, Tempe, AZ GOIN33/574 (2006.01) (US); Ray Akhavan, Haymarket, VA CI2O I/68 (2006.01) (US) (52) U.S. Cl. CPC ........ G0IN33/57434 (2013.01): CI2O I/6886 (21) Appl. No.: 14/124.548 (2013.01) USPC .............................. 506/9; 435/7.92; 435/723 (22) PCT Fled: Jun. 7, 2012 (57) ABSTRACT (86) PCT NO.: PCT/US 12/41387 Biomarkers can be assessed for diagnostic, therapy-related or S371 (c)(1), prognostic methods to identify phenotypes, such as a condi (2), (4) Date: Mar. 24, 2014 tion or disease, or the stage or progression of a disease, select candidate treatment regimens for diseases, conditions, dis ease stages, and stages of a condition, and to determine treat Related U.S. Application Data ment efficacy. Circulating biomarkers from a bodily fluid can (60) Provisional application No. 61/494,196, filed on Jun. be used in profiling of physiological states or determining 7, 2011, provisional application No. 61/494,355, filed phenotypes. These include nucleic acids, protein, and circu on Jun. 7, 2011, provisional application No. 61/507, lating structures Such as vesicles, and nucleic acid-protein 989, filed on Jul. 14, 2011. complexes. 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E. :au?e Elseratant Patent Application Publication Aug. 14, 2014 Sheet 11 of 22 US 2014/0228233 A1 swax. sws: & Patent Application Publication Aug. 14, 2014 Sheet 12 of 22 US 2014/0228233 A1 & SS uds N S ¿n?a.SS SS N. S ae ŠašŠ ()euuseid?••~----- ! Patent Application Publication Aug. 14, 2014 Sheet 13 of 22 US 2014/0228233 A1 s s &x. XXXX-XXX-XXXX-XXXX-XXXX-XXX-XXX-X 8. Patent Application Publication Aug. 14, 2014 Sheet 14 of 22 Patent Application Publication Aug. 14, 2014 Sheet 16 of 22 US 2014/0228233 A1 SYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY-SYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY Patent Application Publication Aug. 14, 2014 Sheet 17 of 22 US 2014/0228233 A1 VSOdpeÐH HI«pis-lawX. HL<HWNX ?Idues ÎHI>IHWX Patent Application Publication Aug. 14, 2014 Sheet 18 of 22 US 2014/0228233 A1 g 3H H. e CC O h CD .9 V CD D S AIAI)SueS Patent Application Publication Aug. 14, 2014 Sheet 19 of 22 US 2014/0228233 A1 Patent Application Publication Aug. 14, 2014 Sheet 20 of 22 US 2014/0228233 A1 Vesicle Test Negatives Converting false negatives to true positives improves sensitivity True Negatives False Negatives Use payload to identify true positives False True Negatives Positives Vesicle Test Positives Converting false positives to true negatives improves specificity False True Positives Positives Use payload to identify true positives True False Negatives Positives • Mishandled samples • Undiagnosed disease • Confounding disease FIG. 13A-B Patent Application Publication Aug. 14, 2014 Sheet 21 of 22 US 2014/0228233 A1 tio Z. Patent Application Publication Aug. 14, 2014 Sheet 22 of 22 US 2014/0228233 A1 3. e e s k s c s s y N star & LeoS8.30 GSS Ae e3e3Selo QSS Ae 8. L & O e C s * V • V g CX D O CD 5 s . * ?a %, L k s 3380Saoli nSS 8Ae- 33480Seol (SSS We s * &% reas wes - g5 ic % & eu83Sejol (SSg. We 308) Sejo (SSg Aes US 2014/0228233 A1 Aug. 14, 2014 CIRCULATING BOMARKERS FOR CANCER 0007. The identification of specific biomarkers, such as DNA, RNA and proteins, can provide biosignatures that are CROSS REFERENCE used for the diagnosis, prognosis, or theranosis of conditions 0001. This application claims the benefit of U.S. Provi or diseases. Biomarkers can be detected in bodily fluids, sional Patent Application Nos. 61/494,196, filed Jun. 7, 2011; including circulating DNA, RNA, proteins, and vesicles. Cir 61/494,355, filed Jun. 7, 2011; and 61/507,989, filed Jul. 14, culating biomarkers include proteins such as PSA and 2011; all of which applications are incorporated herein by CA125, and nucleic acids such as SEPT9 DNA and PCA3 reference in their entirety. messenger RNA (mRNA). Circulating biomarkers can be 0002 This application is a continuation-in-part of Inter associated with circulating vesicles. Vesicles are membrane national Patent Application PCT/US2012/025741, filed Feb. encapsulated structures that are shed from cells and have been 17, 2012, which application claims the benefit of U.S. Provi found in a number of bodily fluids, including blood, plasma, sional Patent Application Nos. 61/446.313, filed Feb. 24. serum, breast milk, ascites, bronchoalveolar lavage fluid and 2011: 61/501,680, filed Jun. 27, 2011: 61/471,417, filed Apr. urine. Vesicles can take part in the communication between 4, 2011: 61/523,763, filed Aug. 15, 2011; and 61/445,273, cells as transport vehicles for proteins, RNAs, DNAs, viruses, filed Feb. 22, 2011; all of which applications are incorporated and prions. MicroRNAs are short RNAs that regulate the herein by reference in their entirety. transcription and degradation of messenger RNAS. MicroR 0003. This application is also a continuation-in-part of NAs have been found in bodily fluids and have been observed International Patent Application PCT/US2011/048327, filed as a component within vesicles shed from tumor cells. The Aug. 18, 2011, which application claims the benefit of U.S. analysis of circulating biomarkers associated with diseases, Provisional Patent Application Nos. 61/374,951, filed Aug. including vesicles and/or microRNA, can aid in detection of 18, 2010: 61/379,670, filed Sep. 2, 2010: 61/381,305, filed disease or severity thereof, determining predisposition to a Sep. 9, 2010: 61/383,305, filed Sep. 15, 2010: 61/391,504, disease, as well as making treatment decisions. filed Oct. 8, 2010: 61/393,823, filed Oct. 15, 2010: 61/411, 0008 Vesicles present in a biological sample provide a 890, filed Nov. 9, 2010: 61/414,870, filed Nov. 17, 2010; Source of biomarkers, e.g., the markers are present within a 61/416,560, filed Nov. 23, 2010: 61/421,851, filed Dec. 10, vesicle (vesicle payload), or are present on the Surface of a 2010: 61/423,557, filed Dec. 15, 2010: 61/428,196, filed Dec. vesicle. Characteristics of vesicles (e.g., size, Surface anti 29, 2010; all of which applications are incorporated herein by gens, determination of cell-of-origin, payload) can also pro reference in their entirety. vide a diagnostic, prognostic or theranostic readout. There 0004. This application is also a continuation-in-part of remains a need to identify biomarkers that can be used to International Patent Application PCT/US2011/026750, filed detect and treat disease. microRNA, proteins and other biom Mar. 1, 2011, which application claims is a continuation-in arkers associated with vesicles as well as the characteristics of part application of U.S. patent application Ser. No. 12/591, a vesicle can provide a diagnosis, prognosis, or theranosis. 226, filed Nov. 12, 2009, which claims the benefit of U.S. 0009. The present invention provides methods and sys Provisional Application Nos. 61/114,045, filed Nov. 12, tems for characterizing a phenotype by detecting biomarkers 2008: 61/114,058, filed Nov. 12, 2008: 61/114,065, filed Nov. that are indicative of disease or disease progress. The biom 13, 2008: 61/151,183, filed Feb. 9, 2009: 61/278,049, filed arkers can be circulating biomarkers including without limi Oct. 2, 2009: 61/250,454, filed Oct. 9, 2009; and 61/253,027 tation vesicle markers, protein, nucleic acids, mRNA, or filed Oct. 19, 2009; and which application also claims the microRNA. The biomarkers can be nucleic acid-protein com benefit of U.S. Provisional Application Nos. 61/274,124. plexes. filed Mar. 1, 2010: 61/357,517, filed Jun. 22, 2010: 61/364, 785, filed Jul. 15, 2010; all of which applications are incor SUMMARY porated herein by reference in their entirety. 0010 Disclosed herein are methods and compositions for 0005. This application is also a continuation-in-part of characterizing a phenotype by analyzing circulating biomar International Patent Application PCT/US2011/031479, filed kers, such as a vesicle, microRNA or protein present in a Apr. 6, 2011, which application claims the benefit of U.S. biological sample. Characterizing a phenotype for a subject Provisional Patent Application Nos. 61/321,392, filed Apr. 6, or individual may include, but is not limited to, the diagnosis 2010: 61/321,407, filed Apr. 6, 2010: 61/332,174, filed May of a disease or condition, the prognosis of a disease or con 6, 2010: 61/348,214, filed May 25, 2010, 61/348,685, filed dition, the determination of a disease stage or a condition May 26, 2010: 61/354,125, filed Jun.