US 201503 15643A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0315643 A1 O'Garra et al. (43) Pub. Date: Nov. 5, 2015 (54) BLOODTRANSCRIPTIONAL SIGNATURES Publication Classification OF ACTIVE PULMONARY TUBERCULOSS AND SARCODOSIS (51) Int. C. CI2O I/68 (2006.01) (71) Applicants: BAYLOR RESEARCH INSTITUTE, (52) U.S. C. Dallas, TX (US); MEDICAL CPC ............ CI2O I/6883 (2013.01): CI2O I/6886 RESEARCH COUNCIL, Swindon (2013.01); C12O 2600/158 (2013.01); C12O (GB); IMPERIAL COLLEGE 2600/16 (2013.01); C12O 2600/1 18 (2013.01); HEALTHCARE NHS TRUST, London C12O 2600/1 12 (2013.01); C12O 2600/106 (GB) (2013.01) (72) Inventors: Anne O'Garra, London (GB); Chloe (57) ABSTRACT Bloom, London (GB); Matthew Paul The present invention includes a method of determining a Reddoch Berry, London (GB); Jacques lung disease from a patient Suspected of sarcoidosis, tuber F. Banchereau, Montclair, NJ (US); culosis, lung cancer or pneumonia comprising: obtaining a Damien Chaussabel, Bainbridge Island, sample from whole blood of the patient suspected of sarcoi WA (US); Viginia Maria Pascual, dosis, tuberculosis, lung cancer or pneumonia; detecting Dallas, TX (US) expression of (although not exclusive) six or more disease (21) Appl. No.: 14/651,989 genes, markers, or probes selected from SEQID NOS.: 1 to 1446, wherein increased expression of mRNA of upregulated (22) PCT Fled: Dec. 13, 2013 sarcoidosis, tuberculosis, lung cancer and pneumonia mark ers of SEQID NOS.: 1 to 1446 and/or decreased expression (86) PCT NO.: PCT/US2013/075097 of mRNA of downregulated Sarcoidosis, tuberculosis, lung cancer or pneumonia markers of SEQ ID NOS.: 1 to 1446 S371 (c)(1), relative to the expression of the mRNAs from a normal (2) Date: Jun. 12, 2015 sample; and determining the lung disease based on the expression level of the six or more disease markers of SEQID Related U.S. Application Data NOS.: 1 to 1446 based on a comparison of the expression (60) Provisional application No. 61/736,908, filed on Dec. level of sarcoidosis, tuberculosis, lung cancer, and pneumo 13, 2012. 18. Patent Application Publication Nov. 5, 2015 Sheet 1 of 21 US 2015/0315643 A1 SETTWACJEZIT\/WHON STOHINOO| WINOWñENd£ 8|| SISOGIOOHWS© NEONVOONQTNo.. Patent Application Publication Nov. 5, 2015 Sheet 2 of 21 US 2015/0315643 A1 Patent Application Publication US 2015/0315643 A1 STOHINOO||. NEONVOONQTNo.. WINOWIEN?? SISOGIOOHWS© : S. S S & &S Patent Application Publication Nov. 5, 2015 Sheet 4 of 21 US 2015/0315643 A1 SISOGIOOHWSENILOW? SISOO||OOHWSHALLOW-NON }|E|ONVO9NITT Patent Application Publication Nov. 5, 2015 Sheet 5 of 21 US 2015/0315643 A1 p40.001 p<0.001 p<0.001 p<0.01 p<0.001 p40.05 1000 p40.05 p<0.001 800 WEIGHTED MOLECULAR 600 DISTANCE 400 TO HEALTH 200 CONTROL ACTIVE PNEUMONIA SARCOD TB NON-ACTIVE CANCER SARCOD FIG. 3B FIG. 4A-1 FIG. 4A-2 FIG. 6A-1 FIG. 6A-2 FIG. 4 FIG. 6 Patent Application Publication Nov. 5, 2015 Sheet 6 of 21 US 2015/0315643 A1 FIG. 4A-1 O&O G (900 G | O Q O OG G eos ooooooooo doooooo oo Ooooooel (33 () (366) (3 OOC) OG E)(3G) () G | O (3G) (C) () (3G) (3)O 3 (3 e G () () O (GSO) () ()(36 () (36) () (OOG) (3G) oooooood (c)(3) () () (336:33Ooooooooooooooo (333 (36)(3)(363.36 (3 (33)(3)(33G)3&63()eeeeoo pool (33333opio &o OOOO OO o OOOoel O OOO OO OO koo o (3G) () ()() () ()() () O (E) () () ()() () Q oo o ode (E) () O OO e Oc (33 CE) 2 (3 (3 (3) O o d (3G) H O3 (33 (3)(3 (3G) () ()(3) (3) ()() " () () ()() () (3) () eO & Ge e o Q G GQ e o oo oo od 363 () (3) GE) () () () () () O GE) o oooooo() ()() (3) odo oo o o () GE) (SG) () ()() & () () soo() o() ()()so e() o lo o o do() NE TB ACTIVE SARCODOSIS NON-ACTIVE SARCOD Patent Application Publication Nov. 5, 2015 Sheet 7 of 21 US 2015/0315643 A1 FIG. 4A-2 3. Q() () M4.10 B-CELLS ke oooo eke oooooo M41M9.2 TCELLsB-CELLS 3O6) M5.15 NEUTROPHILS M4.11 PLASMA CELLS M4.14 MONOCYTES pooe GE M11 PLATELETS 6 M2.3 ERYTHROCYTES OG 6.) M3.1 ERYTHROCYTES 38G)6(3)() (33 QQ M36 CYTOTOXCINK M7.21 CYTOTOXC O M12 F INTERFERON M34 IFN MODULES M5.12 LIFN (3) Q M7.18 IMMUNOSUPRESSION G) M8.61 IMMUNE RESPONSES eO M8.89 IMMUNE RESPONSES b M934 MMUNOSUPRESSION 3.33(3) (3)(33 (33 M3.2 |NFLAMMATION NFLAMMATION M42 INFLAMMATION 4 MODULES a M4.13 NFLAMMATION E M5.1 INFLAMMATION M722 NFLAMMATION () () ( M7.24 LYMPHOCYTEACTIVATION M2.1 CELL CYCLE M22 CELL CYCLE M3.3 CELL CYCLE 6: OO M3.5 CELL CYCLE M6.11 CELL CYCLE M6.13 CELL DEATH M6.16 CELL CYCLE () d M76 PROLIFERATION O M77 PROLIFERATION M78 CELL CYCLE (3)(E)(3G)3 M7.16 DCIAPOPTOSIS 6 O M5.10 MIT RESPIRATION M6.2 MITOCHONDRIAL RESPIRATION k d O M6.12 MITOCHONDRIAL STRESS ====/vvy u/ O OVEREXPRESSED PNEUMONIA LUNG CANCER (3 & 8 (3) Q) O UNDEREXPRESSED 100 908070 60504030 20 PERCENTAGE PROBE (P<0.05) Patent Application Publication Nov. 5, 2015 Sheet 8 of 21 US 2015/0315643 A1 p<0.001 p40.001 p<0.001 p<0.001 p<0.05 p<0.001 p40.001 pCO.001 p40.001 pCO.001 cuo p40.001 p40.001 ly 50 4 s: 40 HS i? 3: 3 O cod 30 E R 5 2 e c 20 e f : 10 f : 1 5 O O NON-ACTIVE CANCER NON-ACTIVE CANCER SARCOD SARCOID ACTIVE PNEUMONIA ACTIVE PNEUMONIA SARCOD SARCOD FIG. 4B FIG. 4C p<0.001 p40.001 p<0.001 p<0.05 P-0001 p<0.001 P-0001 p<0.001 if 30 p-0001p-0001 if 25 p-0001p-0001 1 D S 5 SB 2.0 5 20 e Z C2 E 235 s. 1.5 a PS 10 3. H sas Z. ise S 0.5 32 s O 0.0 4 n. NON-ACTIVE CANCER 4. NON-ACTIVE CANCER SARCOD SARCOD ACTIVE PNEUMONIA ACTIVE PNEUMONIA SARCOD SARCOD FIG. 4D FIG. 4E Patent Application Publication Nov. 5, 2015 Sheet 9 of 21 US 2015/0315643 A1 FIG. 5A PERCENTAGE OF GENES IN PATHWAY O 20 40 60 TB ACTIVE SARCOD EIF2 SIGNALING PNEUMONIA (UNDER-ABUNDANT) CANCER O 5 10 15 -log (B-H p-value) PERCENTAGE OF GENES IN PATHWAY O 20 40 60 TB -NN ACTIVE SARCOID - IFNSIGNALING PNEUMONIA (OVER-ABUNDANT) CANCER O 5 10 15 -log (B-H p-value) PERCENTAGE OF GENES IN PATHWAY O 20 40 60 TB-NN ROLE OF PRRS IN ACTIVE SARCOD RECOGNITION OF PNEUMONIA BACTERIA AND VIRUSES (OVER-ABUNDANT) CANCER O 5 10 15 -log (B-H p-value) PERCENTAGE OF GENES IN PATHWAY O 20 40 60 TB -NN ANTIGEN ACTIVE SARCOID - PRESENTATION PNEUMONIA PATHWAY (OVER-ABUNDANT) CANCER O 5 10 15 -log (B-H p-value) Patent Application Publication Nov. 5, 2015 Sheet 10 of 21 US 2015/0315643 A1 GIOOLIHOOOOn10)--/ @@º@z STIETOTIN Patent Application Publication Nov. 5, 2015 Sheet 11 of 21 US 2015/0315643 A1 GIOOLIHOOOOnT9X–—/ STIETOTIN Patent Application Publication Nov. 5, 2015 Sheet 12 of 21 US 2015/0315643 A1 "OIH[?NET)|×]VINOWITEINdCIS Patent Application Publication Nov. 5, 2015 Sheet 13 of 21 US 2015/0315643 A1 GIOOLHOOOOn10)--/ X @ "OIHEFNEI)|×]}|E|ONY/OSONTOTEIS INVOIN?n8W-HECINQÑ„No.,/*%\€)sz Patent Application Publication Nov. 5, 2015 Sheet 14 of 21 US 2015/0315643 A1 FIG. 6A-1 O O o O Ol 6 (3. O Ole o e o e g g o el o e o O & ele o og o O O 2 o ogo O O o O O e e o so o ol go o o O O O Q Q O 99 () O O e e () e o O ele o (3) () 2 O O ( 0 () () ( e. lo is o 6 o 6 6 o O 6 lo 35CD () () e Q goQ oo H5 Q Q Q lo (3) o (E) (3 e o O o O O o o o A B C D E PRE-TREATMENT POST-TREATMENT PRE-TREATMENT v=v-7 PNEUMONIA Patent Application Publication Nov. 5, 2015 Sheet 15 of 21 US 2015/0315643 A1 FIG. 6A-2 O O Go O G M410 BCELLS M9.2 B-CELLS e Q O Ole e M4.1 T-CELLS O O Ole O M5.15 NEUTROPHILS M4.11 PLASMA CELLS M4.14 MONOCYTES O9 O M1.1 PLATELETS O M2.3 ERYTHROCYTES M3.1 ERYTHROCYTES () elo M3.6 CYTOTOXCINK M7.21 CYTOTOXC O () (3 G M12 IN INTERFERON 999 Q M3.4 IFN r- MODULES M5.12 IFN (D seesO () () () M7.18 IMMUNOSUPRESSION () o () M8.61 IMMUNE RESPONSES () M8.89 IMMUNE RESPONSES G3 G3 (3 & O M32MSYNSESSION NFLAMMATION INFLAMMATION M42 NFLAMMATION 1. MODULES O ()o ()ee () (3e O9 M4.13 NFLAMMATION Ole O e M5.1 NFLAMMATION M7.22 NFLAMMATION olo de :: M7.24 LYMPHOCYTEACTIVATION M2.1 CELL CYCLE |o o e M2.2 CELL CYCLE OO M3.3 CELL CYCLE M3.5 CELL CYCLE o o?e o o M6.11 CELL CYCLE 6 M6.13 CELL DEATH oo o o M6.16 CELL CYCLE O M7.6 PROLIFERATION () o|o o o M7.7 PROLIFERATION M7.8 CELL CYCLE M7.16 DCIAPOPTOSIS olo e as M5.10 MIT RESPIRATION () () M6.2 MITOCHONDRIAL RESPRATION (3 l (; 6 (3) : M6.12 MITOCHONDRIAL STRESS 32 52 62 7212 23 33 4243 PATIENTID INADEQUATE GOOD TREATMENT TREATMENT O OVEREXPRESSED RESPONSE RESPONSE 6 (8 & 3) (3) () (O UNDEREXPRESSED =w=/ 100908070 60504030 20 SA RCODOSIS PERCENTAGE PROBE (P<0.05) Patent Application Publication Nov.