THETWO TORTOITUUS MUUTUU20180022800A1 TONONI MITIN ( 19) United States (12 ) Patent Application Publication (10 ) Pub. No. : US 2018/ 0022800 A1 West et al. (43 ) Pub . Date : Jan . 25 , 2018 (54 ) BIOMARKER Publication Classification ( 51) Int. Ci. ( 71) Applicant: ISIS INNOVATION LIMITED , CO7K 16 /24 ( 2006 . 01 ) Oxford (GB ) A61K 31 / 56 ( 2006 .01 ) A61K 38 / 17 ( 2006 .01 ) GOIN 33868 (2006 . 01 ) (72 ) Inventors : Nathaniel Richard West, Oxford (GB ) ; A61K 38 /20 ( 2006 .01 ) Benjamin Michael Joseph Owens, (52 ) U . S . CI. Oxford (GB ) ; Ahmed Nabil Hegazy , CPC . .. CO7K 16 / 248 ( 2013 .01 ) ; GOIN 33 /6869 Oxford (GB ) ; Fiona Margaret Powrie , ( 2013 .01 ) ; A61K 38 / 204 ( 2013 . 01 ) ; A61K Oxford (GB ) 38 / 1793 ( 2013 .01 ) ; CO7K 16 / 241 ( 2013 .01 ) ; A61K 31 /56 ( 2013 .01 ) ; GOIN 2800 / 52 (2013 .01 ) ; GOIN 2800 /065 (2013 .01 ) ; COZK ( 21) Appl . No. : 15 /547 , 154 2317 / 76 ( 2013 . 01 ) ; GOIN 2333 / 5412 ( 2013. 01 ) ; CO7K 2317 / 24 (2013 .01 ) ; A61K ( 22 ) PCT Filed : Jan . 28 , 2016 2039 / 505 ( 2013 .01 ) ( 86 ) PCT No .: PCT /GB2016 /050185 (57 ) ABSTRACT The invention relates to methods of treating chronic intes $ 371 (c ) ( 1 ) , tinal inflammation and /or inflammatory bowel disease by ( 2 ) Date : Jul . 28 , 2017 administering an antagonist of oncostatin - M (OSM ) and / or OSM receptor - B (OSMR ) . The invention also relates to ( 30 ) Foreign Application Priority Data methods for diagnosing or prognosing chronic intestinal inflammation and /or inflammatory bowel disease in an indi Jan . 29 , 2015 (GB ) .. .. .. .. .. .. .. .. 1501480 .6 vidual and for predicting whether or not an individual will Jan . 29 , 2015 (GB )) .. .. .. .. .. .. .. .. .. .. .. .. .. 1501511 . 8 respond to an anti - TNFa therapy . The methods comprise Dec . 4 , 2015 (GB ) .. .. .. .. .. .. .. .. .. .. 1521446 . 3 measuring OSM and / or OSMR in the individual. Patent Application Publication Jan . 25 , 2018 Sheet 1 of 34 US 2018 /0022800 A1 Figure 1 45 candidate cytokines Colitis versus steady state ( fold change with t- testing ) False discovery rate (10 % ) filtering for significant hits DSS TNBS (C57BL / 6 ) (BALB / C ) 1 / 15 119 1118 1124 Tgfb3 Osm Csf1 / l1a Csf2 Il 16 Ctgf 116 Tnfsf14 1111 Tnf (Light ) Tgfb1 Csf3 112a [117d Ita Ifna /116 121 Ltb Ifnz 1117a7a 1122 Tafb2 1110 1117b 17 Baff Abcb1a4 / H . bilis (FVB ) Patent Application Publication Jan . 25 , 2018 Sheet 2 of 34 US 2018 / 0022800 A1 Figure 2 B CAECAL Osm Osmr EXPLANT CONTENTS * * * * * * 0 .067 ** * * 100 * * 507 * * ; 0 .04 ExpressionrelativetoHort (w/6d)WSO ; ; 0 . 02 Te od CONTROLYCOLITIS CONTROLYCOLITIS CONTROL700V/SI1 CONTROL COLITIS P+7 - 2 4 6 - 6 - 4 2 - 1 2 4 6 - 6 4 2 4 Osm r = 0 . 92 44 r = 0 .81 24 r= 0 .82 ad p < 0 .0001 od p < 0 .0001 -60 p < 0 .0001 1/ 16 - Tnf Patent Application Publication Jan . 25 , 2018 Sheet 3 of 34 US 2018 / 0022800 A1 Figure 3 207 Osm 67 Osmr BB T Relativeexpression 2 Histopathologyscore Q ??? 0 7 14 28 0 7 14 28 0 7 14 28 Day Day Day ? Osmr ** * * * 0 . 087 * * * * * * * * 0 .06 Healthy ExpressionrelativetoHprt Mild /moderate 0 .04 colitis 0 .024 Severe colitis ?????? 0 .000 Patent Application Publication Jan. 25 , 2018 Sheet 4 of 34 US 2018 / 0022800 A1 Figure 4 D tttt * * * * * * * * * * * * * * * * * * * * * 5 * * * * * * * * ? tttt ? OSM 4 OSM Expressionrelativeto|controlmedian(log2) 3 index 1 A sition ???? Q seeire reaonCates HD. 2 nactive IBD , ? control (n = 13 ) uninvolved site ( n =21 ) I active IBD ( n = 44 ) A IBD in remission ( n = 14 ) OSM index BOSMOSMR* * * * * * * * * * * * [ ? tttt 115 * * * * * ¥¥ | * * ** 0 * * * * * * * controlmedian(log2) ? 104 Expressionrelativeto * * * * * * 54?+ JPG - ? | ??L ? control ( n = 13 ) ? quiescent IBD ( n= 27 ) mild - moderately active IBD ( n = 29 ) ? severely active IBD ( n = 9 ) Patent Application Publication Jan . 25 , 2018 Sheet 5 of 34 US 2018 / 0022800 A1 Figure 5 CD UC r = 0 . 90 10 r= 0 .87 195 p < 0 .0001 p < 0 . 0001 OSM 5 10 S100A8 UC om r = 0 .89 57 p < 0 .0001 OSM -5 / CD r = 0 . 91 L - 101 p <0 . 0001 - 100 S100A9 Patent Application Publication Jan . 25 , 2018 Sheet 6 of 34 US 2018 / 0022800 A1 Figure 6 A OSM * * * * OSMR* * * * * * * * * * * * control (n = 13 ) OUC ( n = 24 ) Expressionrelativetocontrolmedian(logo) CD ( n = 19 ) -?FM0 H OO IBD versus controlmucosa ? SIGNIFICANT TOSM ? difference(+/-S.em) CSF3 ? 1L6 ILA IL1B Meanfoldexpression CHIENGJENG qm7000 RIL26 APRIL MOTU p - value Patent Application Publication Jan. 25 , 2018 Sheet 7 of 34 US 2018 / 0022800 A1 Figure 7 OSMR * * * * 0 . 61 | * * 0 .44 Relativeexpression(logo) ??R 0.21 ? -0 . 4 IT | - 0 . 61 ? No pouchitis ( n = 16 ) Pouchitis ( n =40 ) | Familial adenomatous polyposis (n = 18 ) Patent Application Publication Jan . 25 , 2018 Sheet 8 of 34 US 2018 / 0022800 A1 Figure 8 D OSM OSMR 067 nsns malemale 67 - p = 0. 5870 female p =0 .9908 I ? H ns IT 3- 1 AT controlmedian(loga) . controlmedian(log) Expressionrelativeto . relativetoExpression . TO OSM OSMR age at diagnosis (years ) COSM OSMR 67 p = 0 .7985 49 p = 0 . 3459 H Expressionrelativetocontrolmedian(log2) ??? H 5-10 >10 disease duration ( years ) Patent Application Publication Jan . 25 , 2018 Sheet 9 of 34 US 2018 / 0022800 A1 Figure 9 D OSM OSMR ? 8 ] p = 0 . 1133 ' 1 p = 0 .4149 - q 1 T T controlmedian(log) 0 Expressionrelativeto À H 0 Ñ serum CR OSM OSMR 07 p = 0 .4794 47 p = 0 .5646 controlmedian(log2) I 341 Expressionrelativeto ??? H PB leukocytes ( 109/ 1 ) Patent Application Publication Jan . 25 , 2018 Sheet 10 of 34 US 2018 /0022800 A1 Figure 10 Purine synthesis inhibitors Aminosalicylates Steroids 67 ns 64 ns ns ns controlmedian(log2) ns40 nsns ns Expressionrelativeto III II 24 OSM OSMR OSM OSMR OSM OSMR Biologics ( anti- TNF ) Surgery 87 _ ** ** * * * treated walins controlmedian(log2) ins 1 * O untreateduntreated Expressionrelativeto 54 iliOSM OSMR OSM OSMR Patent Application Publication Jan . 25 , 2018 Sheet 11 of 34 US 2018 /0022800 A1 Figure 11 A infliximab responsive infliximab refractory Total / 19 % cohort 48 % 52 % p < 0 . 0001 ( n =61 ) 81 % 94 % CD p < 0. 0001 ( n = 37 ) 100 % ) (58 % 42 % 100 % OSM tertile : 1st 2nd - 3rd 4th OSM * * * * IL1B - D * * * OSMR -ON * * * IL6 - 7 IL17A - * TNF - 5 IFNG - 5 IL22 - 3 IL12B - IL4 - 6 IL13 IL12A IL2341 ó 20 40 60 80 Odds ratio (IFX failure vs success ) Patent Application Publication Jan . 25 , 2018 Sheet 12 of 34 US 2018 /0022800 A1 Figure 12 Responsive Refractory A * * * * NS 207, ? ? O ? IBOWODO Before ? infliximab After OSMindexexpression infliximab p -value OSM INDEX HA 0 .0000052 IL17A 0 .0026 OSM 0 . 0002 OSMR 0 . 000053 146 H 0 . 038 IL1B H 0 .039 IL22 JENG 1112B IL12A 11O TNF ? . CSF2 0 - IL13 ho IL23A ??? 1L4 - 1 12 / 34 - 6 - 4 - 2 0 2 1234 Mean change post- IFX Patent Application Publication Jan . 25 , 2018 Sheet 13 of 34 US 2018 /0022800 A1 Figure 13 GSE16879 , UC / CD GSE16879, CD only 1007 Sensitivity% OSM index Sensitivity% OSM index AUC = 0 .83 404 AUC = 0 . 85 4047 p < 0 .0001 p = 0 .0002 201 n = 61 207 n = 37 © 20 40 60 80 100 0 20 40 60 80 100 100 % - Specificity % 100 % - Specificity % GSE23597FG, UC GSE12251, UC 1007 8047 3 607 Sensitivity% OSM index Sensitivity% 601 OSM index AUC = 0 .87 40 AUC = 0 . 97 p = 0 .0028 p = 0 .0003 n = 32 s 201 n = 21 0 20 40 60 80 100 © 20 40 60 80 100 100 % - Specificity % 100 % - Specificity % Patent Application Publication Jan . 25 , 2018 Sheet 14 of 34 US 2018 /0022800 A1 Figure 14 * * * ** ** * * * Relativeexpression(log) ? ? ? OSM week 0 week 8 week 30 * * * * Relativeexpressionlog() LPI(+ OSMR Ä week 0 week 8 week 30 wk . 8 refractory wk . 8 responsive , wk . 30 refractory wk. 8 responsive , wk . 30 refractory Patent Application Publication Jan . 25 , 2018 Sheet 15 of 34 US 2018 /0022800 A1 Figure 15 DS OSM ??indini??www. IL1B IL1A . wwwwwwwwwwwwww OSMR - H . TIL 17A 3:39 . C wowowomen O www CSF2 . OL. IL6 . .com TNE wwwwwwwwwwwwwwwwww . IL 26 WOODBOB IL22 Wow.col . 9 ADT www. IFNG 000000 . IL12B L21 glowww . wow. www.www IL18 . w . .wwww IL12A w cmsww. www. wwes IL5 www wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwarwe UL7 wwwwwwwwwwwwwwwwwwwwwww lowowowowowowowowowo w owowowowowowo wo wowowowowowowowowowowowowowowowowowowowo wowowowowo w WWw . owo . Command ow wc Maramdamin mimic moldiw . w wwwwwwwww wowowowowwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww www IL15 1L4 ILI w.www.w IL13 wwwwwww powodowawodowe IL27 - 8.90000. IL177 _ IL23A — IENA1 - 7 IFNB LLUVY HITTHE BILLET normal mucosa IBD , IFX - responsive IBD , IFX -refractory D3- 3 Patent Application Publication Jan . 25 , 2018 Sheet 16 of 34 US 2018 /0022800 A1 Figure 16 Th17 cytokines Th1 cytokines OSM-highvslow meandifference(log2) 31 + . 20 +PO . H018Us +80Cv IIITITITITI TIPI 167 CSF2971 IL17A L23A15271 JENG 87171L12A 12186 Significant in Significant in Ulcerative colitis 1 subtype 2 subtypes Crohn 's ( colonic ) + Significant in Crohn ' s (ileal ) * all 3 subtypes B Th1 O Th2 • Th17 IL6 IL22 IL17A (OSM-highvslow) DOÖMNA CSF2 IL1B Mean(+/-SEM)folddifference . IENG OSMR SIGNIFICANT 1 . 25 MTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT Son 10 - 1 10 - 2 10- 3 10 - 4 10- 5 10- 6 p - value Patent Application Publication Jan . 25 , 2018 Sheet 17 of 34 US 2018 /0022800 A1 Figure 17 6x10 - 5 , OSM(pg/cell)D 4x10- 5 . 2x10- 5 poly(1:0 ) MDP Flagellin'LPS PMAlionomycinuntreated MDPPam3CSK4+Pam3CSK4 ?ey? OSM(pg/ml) II ýo LPS notreat poly (l:C ) S.aureus B.longum L .casei AIEC CF..difficileprauznitzii S .epidermidis B. animalis lactisL. acidophilus L.rhamnosus S.enterica E. coli Nissle Patent Application Publication Jan . 25 , 2018 Sheet 18 of 34 US 2018 /0022800 A1 Figure 18 D OSM correlations IL1B Relativeexpression(log2)W | IL12A OSMR IL12B1 . L23A /L6 Correlationcoefficient I + TNE 1 ETNFIFNG Th17 cytokines IL27 O Th1 cytokines . 100 10 - 1 10 - 2 10- 3 10- 4 10- 5 p -value CD14CD14+CD163 +CD14CD163 -CD11cCD14+ -+CD11c E.coliNissleS.epidermidis S.gallolyticus B.longum S.aureus C.difficile B.animalis L.acidophilusF.prauznitzii L.rhamnosus S.enterica AIEC L.casei untreated wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww .