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WO 2015/066640 Al 7 May 2015 (07.05.2015) P O P C T

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WO 2015/066640 Al 7 May 2015 (07.05.2015) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/066640 Al 7 May 2015 (07.05.2015) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12N 15/09 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, PCT/US2014/063736 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 3 November 20 14 (03 .11.20 14) KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (25) Filing Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (26) Publication Language: English SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 61/898,928 1 November 2013 (01. 11.2013) US (84) Designated States (unless otherwise indicated, for every 61/898,932 1 November 2013 (01. 11.2013) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, (71) Applicant: THE RESEARCH INSTITUTE AT NA¬ TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TIONWIDE CHILDREN'S HOSPITAL [US/US]; 700 TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, Children's Drive, Columbus, Ohio 53305 (US). DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, (72) Inventors: SMOYER, William E.; 7465 Lambton Park SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Road, New Albany, Ohio 43054 (US). AGRAWAL, GW, KM, ML, MR, NE, SN, TD, TG). Shipra; 2741 Oakridge Court, Upper Arlington, Ohio 4322 1 (US). RANSOM, Richard F.; 6100 Whitman Published: Road, Reynoldsburg, Ohio 43068 (US). SUNDARARA- — with international search report (Art. 21(3)) JAN, Saraswathi; 8264 Piney Orchard, Blacklick, Ohio 43004 (US). — with sequence listing part of description (Rule 5.2(a)) (74) Agents: BALL, Rebecca L. et al.; Barnes & Thornburg LLP, 11 South Meridian Street, Indianapolis, Indiana 46204 (US). (54) Title: KIT AND METHOD FOR IDENTIFYING INDIVIDUAL RESPONSIVENESS TO STEROID THERAPY OF NEPH ROTIC SYNDROME -log o © FIGURE 1. (57) Abstract: Provided are a kit and a method for identifying a pediatric patient that is resistant to steroid treatment of Nephrotic Syndrome. KIT AND METHOD FOR IDENTIFYING INDIVIDUAL RESPONSIVENESS TO STEROID THERAPY OF NEPHROTIC SYNDROME CROSS-REFERENCE TO RELATED APPLICATIONS This application is an International Application claiming priority under 35 U.S.C. § 119(e) to U.S. Provisional Application Nos. 61/898,928 and 61/898,932, each filed on November 1, 2013, and the contents of which are both incorporated herein by reference. GOVERNMENT LICENSE RIGHTS This invention was made with government support under NIH R01 DK075533, NIH U01 GM092655, and NIH R01 DK095059-01A1 awarded by the National Institute of Diabetes and Digestive and Kidney Diseases. The government has certain rights in the invention. INCORPORATION BY REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY Incorporated by reference in its entirety is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: One 14 KB ACII (Text) file named "232343_SEQList_ST25" created on October 31, 2014. BACKGROUND Nephrotic Syndrome is among the most common kidney diseases seen in both children and adults. Nephrotic Syndrome (NS) is a condition caused by damage to the kidneys that leads to several symptoms, such as swelling, low blood protein levels, high cholesterol and triglyceride levels, but most notably, the release of excess protein in the urine (i.e., proteinuria). NS is characterized by increased permeability in the capillaries of the glomerulus (i.e., the filtering unit of the kidney) which results in low blood protein levels and high levels of urine proteins, since the proteins freely pass from the blood into the urine. Research over the past few decades has identified the importance of renal podocytes, the filtering cells of kidney, as a site of injury in NS. For example, kidneys affected by NS have small pores in the podocytes that are large enough to permit proteinuria. The high urine protein levels disable the glomulerus from safely filtering blood, and results in symptoms of NS. The primary therapy for NS is steroids, such as oral glucocorticoids (GC), which effectively result in remission for the majority of patients. However, approximately 20% of patients either present with, or develop, steroid resistance later in their course of treatment; these patients are classified as having Steroid Resistant Nephrotic Syndrome (SRNS). NS patients who show efficacy with steroid treatment are often diagnosed as having Steroid Sensitive Nephrotic Syndrome (SSNS). The known anti-inflammatory and immunosuppressive effects of glucocorticoids (GCs) have served as indirect evidence that their mechanism of action in NS involves inhibition of soluble mediators released by T lymphocytes. In particular, several podocyte proteins have been identified as playing crucial roles in the development of NS, and a number of rare mutations in these proteins have been identified as causative of the disease or for development of resistance to GC treatment. However, the majority of NS patients present with unknown underlying disease etiology. Similarly, the molecular basis for clinical resistance to GC therapy remains largely unclear. Interestingly, children with SRNS fail to enter remission after prolonged GC steroid treatment, and are at high risk for steroid-induced side effects as well as progression of disease. Approximately 10-30% of SRNS are due to mutations in genes specifically expressed in the filtering cells of kidney, the podocytes, while the etiology of the other approximate 80% of cases is unknown. Identification and development of diagnostic tools to identify SRNS at the time of initial clinical presentation of NS could prevent unnecessary exposure to the toxic effects of steroids and improve the treatment of patients with Nephrotic Syndrome. To design individualized therapies for NS patients, a better understanding of both the complex responses to glucocorticoids (GCs) and the factors that determine susceptibility of the disease and resistance to GC is necessary. Unbiased genome-wide, transcriptome-wide, and proteome-wide systems biology approaches have been identified as key tools to help understand complex diseases, including various forms of primary glomerulopathies. Transcriptome-wide sequencing of RNA enables the assessment of the protein-coding potential of all genes of interest expressed in a tissue. For example, RNAseq is a suitable screening approach for identifying the molecular basis of diseases with unknown etiology, including acquired forms of NS. Identification of the type of NS (steroid sensitive vs. steroid resistant) is crucial to determine the best treatment regimen for NS patients. In particular, the ability to provide patients genetic tests to identify resistant cases of NS. The present invention is able to provide reliable testing to identify patients who have or will develop steroid resistant NS, and thus enable the avoidance of patient exposure to potentially ineffective or adverse medications (i.e., steroids). Described herein are a kit and a method for identifying a patient that is resistant to steroid treatment of Nephrotic Syndrome (NS). The kit and the method comprise reagents for detecting the expression of one or more genes or gene products to identify, diagnose, and/or treat NS in patients with a lack of responsiveness to steroids, such as glucocorticoids (GCs). Further described are gene biomarkers that can differentiate between a patient having Steroid Resistant Nephrotic Syndrome (SRNS) and a patient having Steroid Sensitive Nephrotic Syndrome (SSNS). Specifically, the present invention describes a kit or a method to identify steroid resistance in a patient with NS, wherein the patient is a pediatric patient. SUMMARY Disclosed herein are a kit and a method for identifying a patient with resistance to steroid therapy of Nephrotic Syndrome. In an exemplary embodiment of the kit and the method, the patient is a pediatric patient. In an embodiment of the kit, the kit comprises instructional materials. In one embodiment, the kit comprises a plurality of binding reagents. In one embodiment of the kit, the kit comprises binding reagents , wherein each of the binding reagents specifically binds to a gene product encoded by a gene selected from the group of genes consisting of: RFFL, INPP1, MCM2, CSNK1G1, SIGLEC10, AGPAT6, DCAF8, FAM193A, RSPRY1, KCTD20, BLOC1S3, TOE1, ACAD10, SULF2, RAB8A, NCRNA00294, ZNF318, CDK4, TMEM219, PRKCSH, SLC9A7, LEOl, STX4, PTPRK, GANAB, C170RF63, ZC3H18, MED 14, TRAPPC5, EXOC7, ACINI, ITGAL, SH2D1B, TRMT6, NACC1, RECQL5, ZC3H12D, PRR5L, UBE2J2, TOPBP1, GALNT2, BTN2A2, GPR108, CHMP4B, ALDOA, TRAPPC1, SPRYD3, MTMR14, S1PR5, FAM134C, ALDOC, TCP1, CLCN3, NDUFS1, LGALS9, SUPT5H, JARID2, FAM40A, KLF2, AKIRIN1, ZNF782, OCIAD1, KPNA1, KIAA1033, UBE2W, LOC220930, NCRNA00081, ATP11B, SLC2A1, PIGB, SEPHS2, FGFR10P2, GLIPR2, ARHGEF2, S100A8, H2AFY, SELL, TRIM22, ZC3HAV1, MY05A, ZNF641, SRSF4, ZBTB34, NCOA4, ANTXR2, DDX3X, CHST11, PRNP, SLC35B4, GM2A,
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