(12) Patent Application Publication (10) Pub. No.: US 2015/0133469 A1 O'garra Et Al
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US 2015O133469A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0133469 A1 O'Garra et al. (43) Pub. Date: May 14, 2015 (54) EARLY DETECTION OF TUBERCULOSIS Related U.S. Application Data TREATMENT RESPONSE (60) Provisional application No. 61/610,121, filed on Mar. (71) Applicants: BAYLOR RESEARCH INSTITUTE, 13, 2012. Dallas, TX (US); MEDICAL RESEARCH COUNCIL, Swindon Publication Classification (GB); IMPERIAL COLLEGE (51) Int. Cl. HETICARE NHS TRUST, London CI2O I/68 (2006.01) A63L/33 (2006.01) (72) Inventors: Anne O'Garra, London (GB); Chloe st 7. :08: Bloom, London (GB); Matthew Paul A613 L/4965 (2006.015 Reddoch Berry, London (GB); Robert Wilkinson, Observatory (ZA); Jacques (52) U.S. Cl. F. Banchereau, Montclair, NJ (US); CPC ............ CI2O I/6883 (2013.01); A61 K3I/496 Damien Chaussabel, Bainbridge Island, (2013.01); A61 K3I/4965 (2013.01); A61 K WA (US); Maria Virginia Pascual, 31/455 (2013.01); A61K 31/133 (2013.01); Dallas, TX (US) C12O 2600/158 (2013.01); C12O 2600/I 18 (2013.01) (21) Appl. No.: 14/384,891 (57) ABSTRACT (22) PCT Filed: Mar. 13, 2013 The present invention includes methods for early detection of a treatment response in a patient Suspected of being infected (86). PCT No.: PCT/US2O13/030986 with Mycobacterium tuberculosis. Changes in the blood tran S371 (c)(1), scriptome are detectable within two weeks of the initiation of (2) Date: Sep. 12, 2014 antituberculosis therapy. Patent Application Publication May 14, 2015 Sheet 1 of 66 US 201S/O133469 A1 Fig. A South Africa Active 3 airiers irst Critisetia later Batis is ricsi criteria: Cultire: icositive pirnorary is i{GFA --ye, clirically we fe ya Age years Age > if years a "ser for 1.2 traits Š S S XXX & & P-38 Sangie Carrrk:ced Bri-Estreater No evidence of active is at 2 months 2 weeks. Sarpie S excided: 8 Yissed a Sarnate, i poor quairy contro Patent Application Publication May 14, 2015 Sheet 2 of 66 US 201S/O133469 A1 Fig, 1.8 Eik 8 active 8 patients inclusion criteria As above: Cirica review 23 nonths Connented atti-B treatneri 2 weeks sangle 2 months sainie 4 norths sain pie 6 norths sample Patent Application Publication May 14, 2015 Sheet 3 of 66 US 201S/O133469 A1 SSE SLR.S.E Patent Application Publication US 201S/O133469 A1 QZ(344 Patent Application Publication May 14, 2015 Sheet 5 of 66 US 201S/O133469 A1 IFI Sigilaling Pathay Extracellular Space Cytoplasin f-extreSSed ticleIS 6. 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SS Š treated r as frth 12 ninth 86 signatire Naiss: expression treated Sint Patent Application Publication May 14, 2015 Sheet 23 of 66 US 201S/O133469 A1 Fig. 8B 393 sigraiurg crasse exissio? 86 signitia raise &Xg &Ssign st2.4 Patent Application Publication May 14, 2015 Sheet 24 of 66 US 201S/O133469 A1 Fig. 8C 333 signitie 85 signati & 8 k 88: s s is Sir SS a s is: S- s s Fig. 9 Siricisio: Cfit Cuit repositive pimonary 8 Active TB GRAve., c. icaity weii B} --vis fry Age > 3 years Age Y i8 years rica awaii for 2 norths {in a resies in 12 ri?inths ŠS S S SSS S SS S. N. Š S S. SS SyS, is excide. not fif inclusioi crite fia 13 saw articists SSSS SS S. SS Š S. S SSSX S. S Patent Application Publication May 14, 2015 Sheet 25 of 66 US 201S/O133469 A1 Patent Application Publication May 14, 2015 Sheet 26 of 66 US 201S/O133469 A1 Patent Application Publication May 14, 2015 Sheet 27 of 66 US 201S/O133469 A1 IPA of 565 transcripts feated South Africa 2011 Chart 0. {3: 20 issis 40an 9.SS 60 is3 80 iiiraiei is c\ s s pilify E. AEI E Fi, f. (Conid Patent Application Publication May 14, 2015 Sheet 28 of 66 US 201S/O133469 A1 Patent Application Publication May 14, 2015 Sheet 29 of 66 US 201S/O133469 A1 Patent Application Publication May 14, 2015 Sheet 30 of 66 US 201S/O133469 A1 IPA of 224 transcripts Ireated South Africa 2011 Coiffi 3. - S. SS3, . 40 SSs 60. - S 80 to Untreated t YY: i liteited S. s. s. s s : Plji AAFY is Affif. Fi, ii. (Conid Patent Application Publication May 14, 2015 Sheet 31 of 66 US 201S/O133469 A1 Š SS S Patent Application Publication May 14, 2015 Sheet 32 of 66 US 201S/O133469 A1 §6º0'?gº08ºgog9101 Patent Application Publication May 14, 2015 Sheet 33 of 66 US 201S/O133469 A1 IPA of 711 transcripts icated Stiff Africa 2011 Citri O : 20 -Sg S. 40 SS 60 S 80 iO opw ss. 5 S is filiff ARY FE LAf F. C. (Conti) Patent Application Publication May 14, 2015 Sheet 34 of 66 US 201S/O133469 A1 Fig. 10D 28S Coiffs Kiraining 565 si SA 2. list Fig. 10E SA 2). 2G9 & 2Ci: Cohorts featre it Sigitatre SA 23 Active 8 Signate 2GOS Coorts twe: tapping Weri frar scripts 344 trafscripts Patent Application Publication May 14, 2015 Sheet 35 of 66 US 201S/O133469 A1 Fig. A ketiye Egates.iciusior triteria: latest8tists inclusion crite:ia: {Cite positives to stry $8 {{SRA is, tiricaity wei 8w ye - : W sys Rge x 3 year's Age x 3 yea:S Citics risik is 3 tists {Bica fissists or raisits 38-traits:: &3 Spies i: sats: Sagi. hia &ireita Rative 3 at is fiants 2 : sixtis: 88:8 8:3this six frie S S 2 orths sspie SSSSSSSSS SS S Š SSSSSSSSSSS O Š SS SS S. Patent Application Publication May 14, 2015 Sheet 36 of 66 US 201S/O133469 A1 Fig. 118 Active TB patients inclusion Criteria As above Clinica review & 9 months Pre-treatment Sample Corenced arti treatient 2 weeks. Sample 2 months sample 4 months sample 6 months sample Š ŠSŠŠs Š Y SSSS Š SSSSSSSS SSSSSSSSSSSS: x S. Š Patent Application Publication May 14, 2015 Sheet 37 of 66 US 201S/O133469 A1 Patent Application Publication May 14, 2015 Sheet 38 of 66 US 201S/O133469 A1 Fig. 2C 393 sigrature 86 signature s:::: Fig. 13A Sagit Africa: 2Gi Cohort, gees pierraised to 8diar; i383: ::::::::::::: 88::::::: Patent Application Publication May 14, 2015 Sheet 39 of 66 US 201S/O133469 A1 \f"|8+3A?IOV/8||N3 (1s1)izg9)quoqoOTIOZpo?u/v/unnos peneaunun,unuz?,9,z,xwpeneau-aud Patent Application Publication May 14, 2015 Sheet 40 of 66 US 201S/O133469 A1 Fig.