US 20140378425A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0378425A1 Wilde et al. (43) Pub. Date: Dec. 25, 2014 (54) BOMARKERS FOR DIAGNOSIS OF LUNG Publication Classification DISEASES AND METHODS OF USE THEREOF (51) Int. C. CI2O I/68 (2006.01) (71) Applicant: Veracyte, Inc., South San Francisco, CA A 6LX3/97 (2006.01) (US) A613 L/52 (2006.01) A613 L/442 (2006.01) (72) Inventors: Jonathan I. Wilde, South San Francisco, A 6LX3/573 (2006.01) CA (US); Sharlene Velichko, South San (52) U.S. C. Francisco, CA (US); Catalin CPC .......... CI2O I/6883 (2013.01); A61 K3I/4412 Barbacioru, South San Francisco, CA (2013.01); A61 K3I/573 (2013.01); A61 K (US); James Diggans, South San 31/52 (2013.01); A61K3I/197 (2013.01); Francisco, CA (US); Giulia Kennedy, C12O 2600/158 (2013.01); C12O 2600/I 12 South San Francisco, CA (US) (2013.01) USPC .. 514/179; 506/9:435/7.92; 506/2:435/6.11; (73) Assignee: Veracyte, Inc., South San Francisco, CA 435/6.12: 514/345; 506/16; 514/263.2: 514/562; (US) 702/20 Appl. No.: 14/213,632 (21) (57) ABSTRACT (22) Filed: Mar 14, 2014 The present disclosure provides methods for diagnosis of interstitial lung diseases (ILDS). The present disclosure pro Related U.S. Application Data vides methods for differential diagnosis of idiopathic pulmo (60) Provisional application No. 61/799,754, filed on Mar. nary fibrosis from other ILDs. Compositions and kits useful 15, 2013. in carrying out a Subject method are also provided. Patent Application Publication Dec. 25, 2014 Sheet 1 of 129 US 2014/0378425 A1 Figure 1 DataSet N is 84 3 x 383r x ladiag M. simir SF s Symline artixedcost Lipids: s: if geries Patent Application Publication Dec. 25, 2014 Sheet 2 of 129 US 2014/0378425 A1 eODS Patent Application Publication Dec. 25, 2014 Sheet 3 of 129 US 2014/0378425 A1 Figure 3 Dataset N is 89 i - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - . Siar s Ed's s 8 - f 4 is genes Patent Application Publication Dec. 25, 2014 Sheet 4 of 129 US 2014/0378425 A1 e ODS Patent Application Publication Dec. 25, 2014 Sheet 5 of 129 US 2014/0378425 A1 Figure 5 inpitats 3 $80 -. y : 8 w w w w w w w w w w w w w ' ' ' ' ' ' ' ' ''' ------------------------------------------------ - " - ips: ress Eterface wists r x-r irr 3. -------------------------------------------'-'.'.or orggro-r3ts mor, ... 88: Batatase 3. : : Storage 8wice : to- ---------------------------------------------- Ottp:st Cata Patent Application Publication Dec. 25, 2014 Sheet 6 of 129 US 2014/0378425 A1 Figure 6A Differentially expressed genes between IPF and NSIP using Microarray data. Comprehensive list of markers based on significance (FDR pro.05). A total of 495 markers were found to be significant with this analysis. Log2 fold changes of genes overexpressed in PF as compared to NSIP range from 0.30 to 1.87. Log2 fold changes of genes underexpressed in EPF as compared to NSEP range from -2.43 to -0.28. Overexpressed: ACACB, ACTA2, ACTG2, ADARB1, AHNAK2, AMOT, ANO!, ANO2, ANTXR1, AOC3, ARHGAP 10, ARHGEF25, ATP1A2, ATP B2, Corf 15, C2orf40, C7orf4 C8orf84, CALD, CAP2, CASQ2, CDC42BPA, CDH13, CDH6, CFC B, CNN1, CNTN4, COL21A1, CORO2B, COX7A, CREM, CRIP2, CRYAB, CXorf69, DAAM1, DENND2A, DES, DGKG, DEXDC, DMD, DST, EDIL3, EFHD1, EXOC6B, FABP4, FAM13C, FAM21C, FBXL2, FHL}, FHL5, FRY, GARNL3, GNA, HEY2, HRCTI, HSPB7, HTRF, ICAL, IGF1R, IGFBP5, ITGB4, JAG1, KALRN, KANK2, KIAA 1377, LGR4, LHFP, LMCD1, LMOD1, LPHN3, LRRFP1, LTBP4, LY6G6C, MAP B, MAP7 D3, MARK1, MPDZ, MSRB3, MUSTN MXRA7, MYH MYL9, MYLK, MYOCD, MYOM1, NBPF 10, NDRG2, NET, NEXN, NKD 1, PALLD, PALMD, PARD3B, PBX). PCDHB10, PCDHB3, PDEC, PDE2A, PDE5A, PEG3, PGM5, PHLDB2, PHY HIPL, PKD2, PKIG, PLCB4, PLCE, PLEKHH2, PLN, PPARGC1A, PPFIBP1, PPML, PPP1R 14A, PPP1R3C, PRDMS, PRELP, PREX2, PRKAA2, PRKG 1 PRUNE2, PTCHD4, PTPN14, PTPN2, PTRF, RBM24, RBMS3, REP 15, RGS7BP, RNF180, ROCK2, SDC2, SLN, SORBS1, SUN, SVIL, SYNM, SYNPO2, TAGLN, TBC1D19, TCID-7895852, TCID-7919146, TCID-7981986, TCID-7981988, TCTD-798.1990, TCID-7996260, TCID-8027746, TCID-8031646, TCID-8124498, TCID-8161520, THRA, TEMP3, TMEM47, TNS, TPM1, TPM2, TRPC1, TTLL7, USP2, WDR52, WDR60, ZC3H2B, ZFP28, ZFYVE9, ZNF221, ZNF45, ZNF461, ZNF483, ZNF879, Patent Application Publication Dec. 25, 2014 Sheet 9 of 129 US 2014/0378425 A1 Figure 8 Differentially expressed genes between IPF and NSIP using RNA-Seq, Comprehensive list of markers based on NPSeq analysis of RNASeq data. A total of 160 markers were found to be significant with this analysis. Log2 fold changes of genes overexpressed in IPF as compared to NSP range from 0, 15 to .95. Log2 fold changes of genes underexpressed in IPF as compared to NSP range from -2.30 to -0. 4. Overexpressed. ABI2, AHNAK, AKAP6, AKR1C3, AMOT, AXL, BMPR1A Clorf168, C2Orf40, C5orf4, C7orf58, C8orf84, C9arf25, CAP2, COLAA5, COLAA6, CPQ, CSRP1, DNAJC19, ENSG00000149531, ENSG0000020948. FAM189A1, FAM63B, FHL, FMO2, GAS6, GSTM3. LGR4, LGR6, LIMS2, LMOD1, MSRB3, MXRA7, NACC2, NEK7, NKD 1, NPTXR, NXPH3, NYNRIN, OMA, PALLD, PARD3B, PDFC, PHLDA3, PPML, PPP1R3C, PTCHD4, RBMS3, RSPH3, SCD5, SEPT7, SKAP2, SLC1A7, SVEL, SYNC, TIMP3. TPM1, TRNP, TTLL7, UGP2, ZNF583, ZNF607, ZNF615, ZNF880. Underexpressed, AASS, ABCA3, ACADSB, ACPP, ACSM3, ACSS2, ANLN, ARHGEF38, ATP2C2, B4GALT3, CA 3, CCNF, CDKL2, CEP55, CFTR, CHEK, CISH, COPG, CREB3L1, CSF3R, CXCL17, CXCL3, DERL), DRAM1, DUSP16, EDEM1, ENSG00000137700, ENSG00000224189, ENSG00000225431, ENSG00000228863, ENSG00000248801, ENSG00000248890, ENSG 00000256039, ERN, FADSi, FADS2, FAM20A, FAM40B, FASN, GBF1, HK2, HM13, HOXD1, IL8, KCNQ3, KIF 14, KIF 8B, KIF4A, LAD1, LAMP3, MACROD2, MAPK13, METTL7B, MTRR, MUC21, NUP50, ORM1, PDZK1 EP, PMAIP1, PNKD, POLR2C, POU2F3, PPP1R1B. R3HDMI, RGS16, ROS1, SCN1A, SCTR, SDR16C5, SEC24D, SEMA4A, SERPINA 1 SFTPD, SFXN1, SFXN2, SIAE, SLC5A8, SLC7A 11, SLC7A5, SMC4, SOD2, SRSF6. ST8SIA4, SURF4, TBC1D24, TDRKH, TLR2, TNIP3, TOP2A, TOX, TROAP. TST, TTC39A, YARS, ZDHHC18, ZNF238. Patent Application Publication Dec. 25, 2014 Sheet 19 of 129 US 2014/0378425A1 Figure 10F Underexpressed (continued) TCID-7894200, TCID-7894204, TCID-7894285, TCID-7894355, TCID-7894482, TCID-7894537, TCID-7894562, TCID-7894.575, TCID-7894.639, TCID-7894752, TCID-7895.080, TCID-7895.098, CID-7895.25. TCD-7895153, TCID-7895.223, CD-7895.308, TCD-7895362, TCID-7895.381, TCID-7895.384, TCID-789S448, TCID-7895.505, TCID-7895536, TCID-7895581, TCID-7895.603, TCID-7895751. TCID-7895847, TCID-7895957, TCID-7896098, TCID-7896275, TCID-7896393, TCD-78964 13, TCID-7896439, TCID-7896598, TCID-7896632, TCID-789664, TCID-7896659, TCID-7902685, TCID-7904.048, TCID-7904953, TCID-79.05731, TCID-79 13803, TCID-7914214, TCID-79 6781. TCD-7918048, TCID-7919594, TCD-79.9747, TCID-7919749, TCID-7922523, TCID-7926484, TCID-7927595, TCID-7927704, TCID-7928367, TCID-793.0915, TCID-7932552, TCID-79378.90, TCID-793.8258, TCID-793.8293, TCID-7938.681, TCID-7939.902, TCID-794.0717, ICED-794196). TCD-7942061, TCID-7942877, TCED-794460, TCD-7945942, TCID-794632, TCID-7951339, TCID-7952737, TCID-7953977, TCID-7954310, TCID-795.8826, TCID-796.0338, TCID-796052, TCID-796054, TCID-7961602, TCID-7962341, TCID-7965036. TCID-7965. 10, TCED-7968232, TCID-7969339, TCID-7969531, TCID-7969638, TCID-7970082, TCID-797 1998. TCD-7972803, TCID-7974008, TCID-7974.027, TCID-7974.029, TCID-7975813, TCID-7980906, TCID-798.3054, TCID-7983951, TCID-7989883, TCID-7990755, TCID-799 1171, TCID-7993 179, TCID-7994.091, TCID-7995.377, TCID-7999362, TCID-7999476, TCID-8003075, TCID-8005626, TCID-8005753, TCID-80.11678, TCID-80 13013, TCID-80 13329, TCID-80 13356, TCID-8013523, ICD-805757. TCD-80 19088, TCID-80957, TCED-809709, TCD-8020139, TCID-8020239, TCID-8022243, TCID-8022378, TCID-80225.06, TCID-8022557. TCED-8024566, TCID-8027354, TCID-803566, TCID-8034694, TCID-8037387, TCID-8039084, TCID-8042219, TCID-8042464, TCD-8043498, TCID-8043993, TCID-8045341, TCID-8045343, TCD-8045533, TCID-8045804. TCID-80460:8, TCID-8050213, TCID-8051812, TCID-8054607, TCID-8055348, TCID-8055486, TCID-8056359, TCID-8059744, TCED-8061414, TCID-8063026. TCED-8063408, TCID-8064,857, TCID-8065134, TCID-8065363, TCID-8065756, TCID-8066275, TCID-8066983, TCID-8067877, TCED-8069768, TCID-8071204, TCID-8073680, TCID-8074714, TCID-8074716, TCID-8075693, TCD-8077499, TCD-8082605, TCED-8083455, TCID-8083492, TCID-8083592, TCID-8083848, TCID-8083.893, TCID-8084739, TCD-8090674, TCID-8091 101, TCID-8091444, TCID-8092390, TCID-8093451, TCID-8093974, TCID-8094026, TCID-8094,340, TCID-8094776, TCID-809559, TCID-80322, TCID-802230, TCID-8103975, TCID-8104568, TCID-810607, TCID-8108013, TCD-8108977. TCD-8 12335, TCED-81 12666, TCD-81 13717, TCID-8 14812, TCED-81 15664, TCID-8 15679, TCID-81 16992, TCED-8 7712, TCD-820820, TCID-8 2390, TCID-812 1884, TCD-8122 198, TCID-8122701, TCID-823340, TCID-8123407, TCID-827662, TCID-8127752. TCID-8131512, TCID-8132290, TCID-8132998, TCID-8133070, TCID-8133106, TCID-8133688, TCID-8135585. TCID-8137483, TCID-839816, TCD-8143365, TCID-8:45083, TCID-81.45795, TCID-84639, TCID-8146857, TCID-8 47373, TCD-847990, TCID-81.48040, TCID-8150689, TCID-8150862, TCID-8153041, TCID-815432, TCID-8154719, TCID-8154838, TCID-8155026, TCID-8155376. TCD-8156358, TCID-8160767, TCID-81 61000, TCID-8 62645, TCID-8163710, TCID-8164694, TCID-8165255, TCID-8165646, TCID-8165656, TCID-8: 65658, TCID-8165696, TCID-8681 15, TCID-86936, TCED-8 7098, TCD-87 18O, TCID-8 72082, TCID-8 172266, TCID-817.3156, TCID-8173924. TCTEX1D4, TEAD4, TEK, TFPI, TGIF1, THBD, THSD1, TIPARP, TKT, TLCD1, TLR2, TLR3, TM7SF2, TM7SF4, TMEM100, TMEM116, TMEM125, TMEM130, TMEM139, TMEM14, TMEM16B. TMEM164, TMEM170A, TMEM180, TMEM2, TMEM242, TMEM30B, TMEM41B, TMEM45B, TMEM53, TMEM87A, TMEM88, TMEM97, TMPO, TMPRSS2, TMSB15A, TNFSF10, TNNC, TNNI2. TNNE3, TNNT1, TNNT2, TNS3, TOML Patent Application Publication Dec. 25, 2014 Sheet 27 of 129 US 2014/0378425A1 Figure 12 Differentially expressed genes between NSIP and HP using Microarray data. Markers were selected based on significance (p<0.05) after Benjamini and Hochberg correction for false discovery rate (FDR).