US 20090258848A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2009/0258848A1 Chakravarti et al. (43) Pub. Date: Oct. 15, 2009 (54) BIOMARKERS FOR INFLAMMATORY (30) Foreign Application Priority Data BOWEL DISEASE Dec. 6, 2005 (US) ....................... PCT/USO5/44423 (75) Inventors: Shukti Chakravarti, Lutherville, MD (US): Feng Wu, Lutherville, Publication Classification MD (US) (51) Int. Cl. Correspondence Address: A 6LX 3/573 (2006.01) EDWARDS ANGELL PALMER & DODGE LLP C7H 2L/02 (2006.01) P.O. BOX SS874 CI2O I/68 (2006.01) BOSTON, MA 02205 (US) A6IPI/00 (2006.01) (73) Assignee: THE JOHNS HOPKINS (52) U.S. Cl. ............................. 514/177:536/23.1: 435/6 UNIVERSITY, Baltimore, MD (US) (21) Appl. No.: 11/750,114 (57)57 ABSTRACT The present invention relates to methods of determining (22) Filed: May 17, 2007 inflammatory bowel disease status in a subject. The invention O O further relates to kits for determining inflammatory bowel Related U.S. Application Data disease status in a subject. The invention further related to (60) Provisional application No. 60/801,663, filed on May methods of identifying biomarker for determining inflamma 19, 2006. tory bowel disease status in a Subject. Patent Application Publication Oct. 15, 2009 Sheet 1 of 26 US 2009/0258848A1 Patent Application Publication Oct. 15, 2009 Sheet 2 of 26 US 2009/0258848A1 20 10 O - 10 Component1 FIG 2 FIG. FG. 3A 3B FG. 3 Patent Application Publication Oct. 15, 2009 Sheet 3 of 26 US 2009/0258848A1 FIG. 3A Inflammat ion - - - - - - - - - - - - - - - -- - - - - Patent Application Publication Oct. 15, 2009 Sheet 4 of 26 US 2009/0258848A1 FIG. 3B zinc finger protein-like 1 sorting nexin 4 "serine palmitoyitransferase, long chain base subunit 1" stromal cell derived factor receptor 1 acyl-Coenzyme Abinding domain COntaining 3 thioredoxin domain Containing RAN binding protein 2. Cell cycle progression 8 protein K1AA1012 15kDa selenoprotein "At Pase, H+transporting, lysosomal 13kDa, W1 subunit G isoform 1" "protein phosphatase 2, regulatory subunit B (B56),epsilon isoform" K1AA0372 annexin A7 GRP1-binding protein GRSP1 stress-associated endoplasmic reticulum protein 1 TRAF family member-associated NFKB activator "dollohyl-phosphate mannosytransferase polypeptide 1, catalytic subunit" RAN binding protein 2-like 1 "RAP1A, member of RAS oncogene family "rashomologgene family, member E" flucose-1-phosphate guanylytransferase NIMA(never in mitosis genea)-related kinase 7 mitochondrial ribosomal protein L3 ADP-ribosylation factor-like 1 below ear abOve lysosomal-associated protein transmembrane 4 alpha "proteasome (prosome, macropain) subunit, alpha type, 4" "microtubule-associated protein, RP/EB family, member 1" "coatomer protein Complex, subunit beta 2 (beta prime)" pre-B-cell colony enhancing factor 1 activated RNA polymerase II transcription Contactor 4 "methylene tetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase" KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3 chemokine (C-X-C motif) ligand 3 chemokine (C-X-C motif) ligand 1 chemokine (C-X-C motif) ligand 2 hydroxysteroid (17-beta) dehydrogenase 2 D Component of Complement (adipsin) tripartite motif-containing 3 PTK9L protein tyrosine kinase 9-like (A6-related protein) signal-induced proliferation-associated gene 1 hypothetical protein BC002942 chromosome 22 Open reading frame 3 ataxin 2 related protein mitogen-activated protein kinase kinase kinase 11 "phosphofructokinase, liver" 5-oxoprolinase (ATP-hydrolysing) "ubiquitin-Conjugating enzyme E2M (UBC12 homolog, yeast)" DKFZP566HD73 protein DKFZP586JD619 protein Patent Application Publication Oct. 15, 2009 Sheet 5 of 26 US 2009/0258848A1 CIO Patent Application Publication Oct. 15, 2009 Sheet 6 of 26 US 2009/0258848A1 Patent Application Publication Oct. 15, 2009 Sheet 8 of 26 US 2009/0258848A1 Je-O?) 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Lo C CN CN vr vas O O LLWO (gun As.IIqb) anea uossa.dx eAgee Patent Appl icat ion Publica tion Oct. 15, 2009 Sheet 15 of 26 US 2009/0258848A1 Patent Application Publication Oct. 15, 2009 Sheet 16 of 26 US 2009/0258848A1 s & & f ( FIG. 11D Patent Application Publication Oct. 15, 2009 Sheet 17 of 26 US 2009/0258848A1 OZ O O 0|- 09 OZ V Zueuoduod Patent Application Publication Oct. 15, 2009 Sheet 18 of 26 US 2009/0258848A1 09 0|| ?ueuoduoOZ 0 O 0|- OZ Eueuoduod Patent Application Publication Oct. 15, 2009 Sheet 19 of 26 US 2009/0258848A1 O CN O O 09 Vr Zueuoduod Patent Application Publication Oct. 15, 2009 Sheet 20 of 26 US 2009/0258848A1 <<<<<<<5555 333333scoupupun-NicoccupN.deseyssagebsbSega's 22 22SSAARAACC2C2C2C2 to SassessessSSSSSZZ 25 IL8, CXCL1, CXCL2, CXCL3, NOS2A, CD REG3A, S100AD, HLA-DRB1, & HLA-DMA, LCN2, BF, DMBT1. UC 18 ADD3, CLDN8, ACBC1. 22 STAT1, STAT3, TAP PSME2, PSMB8, CD PSMB9, PSMB10, IFITM1, IFITM3 CASP 10. 12 WEE1, SPON1, THES1. 26 PECAM1, CD79A, POU2AF1, CCL11, PTODS, TNFFSF7, MMP12, TMP1, IF130, NOTCH3. UC UGDH, PCK1, GGH, CCNT2, CHD1, 63 HNF4G, KLF5, MLLT2, MYB, NR3C2, SATB2, ZNF217, TNPO1, SCAMP1, VPS13A, ATP2B1, SLC16A1, SLC26A2, AQP8, GUCA2A. 3 INF 32 Patent Application Publication Oct. 15, 2009 Sheet 21 of 26 US 2009/0258848A1 © <tcocN Normal CDeff UCaff F.G. 14A FIG. 14B Normal CDef UCaff F.G. 14C FIG. 14D —[ETH -#- Normal CDef UCaff F.G. 14E FIG. 14F Patent Application Publication Oct. 15, 2009 Sheet 22 of 26 US 2009/0258848A1 i i i 25 IL8, CXCL1, CXCL2, CXCL3, NOS2A, REG3A, S100A9, HLA-DRBI, HLA-DMA, LCN2, BF, DMBTI 18 ADD3, CLDN8, ACBC1 > 22 STATI, STAT3, TAPPSME2, PSMB8, PSMB9, PSMC10, IFITM1, IFITM3, CASP10 12 WEEI, SPON1. THESI CCL11, PTODS, TNFRSF7, MMP12, TYMPI, IFI30, NOTCH3 63 UDGH, PCK1, GGH, CCNT2, CHD1, HNF&G, KLF5, MLLT2, MYB, NR3C2, SATB2, ZNF217, TNPO1, SCAMPI, VOS13A, ATP2B1, SLC16A1, SLC26A2, ACP8, GUCAZA FIG. 15 Patent Application Publication Oct. 15, 2009 Sheet 23 of 26 US 2009/0258848A1 O) co Normal CDaff UCaff Normal CDaff UCaff s mm. co Normal CDaff UCaff w Normal CDaff UCaff 0.25 4 0.20 3 N 0.15 S S S 2 a 0.10 S 1 0.05 Co* 0.00 O Normal CDaff UCaff Normal CDaff UCaff FIG. 16 Patent Application Publication Oct. 15, 2009 Sheet 24 of 26 US 2009/0258848A1 FIG. 17C Patent Application Publication Oct. 15, 2009 Sheet 25 of 26 US 2009/0258848A1 Patent Appl ication Publication Oct. 15, 2009 Sheet 26 of 26 US 2009/0258848A1 US 2009/0258848 A1 Oct. 15, 2009 BOMARKERS FOR NFLAMMATORY 0007. The present invention provides a method of quali BOWEL DISEASE fying inflammatory bowel disease status in a subject compris ing measuring at least one biomarker in a sample from the RELATED APPLICATIONS Subject. 0008. In one embodiment, the method of resolution 0001. This application claims priority from U.S. Provi involves Surface-Enhanced Laser Desorption/Ionization sional Application No. 60/633,662, filed Dec. 6, 2004: PCT (“SELDI) mass spectrometry, in which the surface of the Application No.: PCT/US2005/44423 filed Dec. 6, 2005; and mass spectrometry probe comprises adsorbents that bind the U.S. Provisional Application No. 60/801,663, filed May 19, markers. 2006, which are incorporated herein by reference in their 0009. In one aspect, the invention provides biomarkers for entirety. inflammatory bowel disease status comprising one or more of the following Markers 1-97, 99-211, 213-264, 266-401 and combinations thereof. These Markers 1-97, 99-211,213-264, BACKGROUND OF THE INVENTION 266-401 are set forth in Table 1-9, which follows and are sometimes referred to herein as biomarkers of Table I or 0002 Crohn's disease (CD) and ulcerative colitis (UC), similar designations. are complex, heterogeneous, multifactorial diseases involv 0010. In one aspect, the invention provides biomarkers for ing genetic, environmental and microbial factors. These inflammatory bowel disease status comprising one or more of inflammatory bowel disease (IBD) subtypes have distinctive Markers 1-97, 99-211, 213-264, 266-401 and combinations etiopathologies yet share clinical and demographic features. thereof. '" As many as 4 million people worldwide suffer from a form 0011.