US 201500 72349A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0072349 A1 Diamandis et al. (43) Pub. Date: Mar. 12, 2015 (54) CANCER BOMARKERS AND METHODS OF (52) U.S. Cl. USE CPC. G0IN33/57484 (2013.01); G0IN 2333/705 (2013.01) (71) Applicant: University Health Network, Toronto USPC ......................................... 435/6.12: 435/7.94 (CA) (57) ABSTRACT A method of evaluating a probability a Subject has a cancer, (72) Inventors: Eleftherios P. Diamandis, Toronto diagnosing a cancer and/or monitoring cancer progression (CA); Ioannis Prassas, Toronto (CA); comprising: a. measuring an amount of a biomarker selected Shalini Makawita, Toronto (CA); from the group consisting of CUZD1 and/or LAMC2 and/or Caitlin Chrystoja, Toronto (CA); Hari the group CUZD1, LAMC2, AQP8, CELA2B, CELA3B, M. Kosanam, Maple (CA) CTRB1, CTRB2, GCG, IAPP, INS, KLK1, PNLIPRP1, PNLIPRP2, PPY, PRSS3, REG3G, SLC30A8, KLK3, NPY, (21) Appl. No.: 14/385,449 PSCA, RLN1, SLC45A3, DSP GP73, DSG2, CEACAM7, CLCA1, GPA33, LEFTY1, ZG16, IRX5, LAMP3, MFAP4, (22) PCT Fled: Mar. 15, 2013 SCGB1A1, SFTPC, TMEM100, NPY, PSCA RLN1 and/or SLC45A3 in a test sample from a subject with cancer; (86) PCT NO.: PCT/CA2O13/OOO248 wherein the cancer is pancreas cancer if CUZD1, LAMC2, S371 (c)(1), AQP8, CELA2B, CELA3B, CTRB1, CTRB2, GCG, LAPP (2) Date: Sep. 23, 2014 INS, KLK1, PNLIPRP1, PNLIPRP2, PPY, PRSS3, REG3G, SLC30A8, DSP GP73 and/or DSG2 is selected; the cancer is colon cancer if CEACAM7, CLCA1, GPA33, LEFTY 1 and/ Related U.S. Application Data or ZG16 is selected, the cancer is lung cancer if IRX5, (60) Provisional application No. 61/611,955, filed on Mar. LAMP3, MFAP4, SCGB1A1, SFTPC and/or TMEM100 is 16, 2012. selected; or the cancer is prostate cancer if NPY. PSCA, RLN1 and/or SLC45A3 is selected; b. comparing the mea Sured amount to a control and detecting an increase in the Publication Classification amount of the biomarker compared to control; and c. identi fying the Subject as having or having an increased probability (51) Int. C. of having the cancer when an increase in the biomarker com GOIN33/574 (2006.01) pared to control is detected. Patent Application Publication US 2015/0072349 A1 |Jop??eroes |pe??uep?sule,old eueSÐÁJe/\ ººqeueÐlunºH?911 auas)un‘HE?IL'II-o:SLSH• |3.Infil Patent Application Publication Mar. 12, 2015 Sheet 2 of 18 US 2015/0072349 A1 O G o GP C s N v- S. C c e-n n oq SS O O SR O U C : 5 D .9- C D o R. h-s Qd (My O O O O OO O O VH (%) AllAsues O S. o CP O N N OY S. g 8O C - 5 S st & u- Ces 9 <C 5 CU2 3 OS Ol Q9 M O O ?y O OO O O OOL O8 O9 Ot/ O O (%) AllAsues Patent Application Publication Mar. 12, 2015 Sheet 3 of 18 US 2015/0072349 A1 FIGURE 4 CUZD1 PCOOOO1 4. O CA19-9 P<0.0001 0 8500 6000 :1 OOO w . 850 600 g 350 1 OO Healthy Benign Cancer Patent Application Publication Mar. 12, 2015 Sheet 4 of 18 US 2015/0072349 A1 FIGURE 5A ROC (Healthy vs Cancer) 3 8 8 S. - CUZD1 (AUC=0.826) S - - CA19.9 (AUC=0.816) 100 80 60 40 2O O Specificity (%) Patent Application Publication Mar. 12, 2015 Sheet 5 of 18 US 2015/0072349 A1 FIGURE 5B 83 ROC (Benign vs Cancer) S. - CUZD1 (AUC=0.849) S - - CA19.9 (AUC=0.827) 100 80 60 40 20 O Specificity (%) Patent Application Publication Mar. 12, 2015 Sheet 6 of 18 US 2015/0072349 A1 FIGURE 5C AUC (95% CI) - a CA 9-9 O84 (0.76-092) - CUZD1+CA19-9 094 (089-099) g- T -- -- O-4 O6 8. -O 1 - Specificaty Patent Application Publication Mar. 12, 2015 Sheet 7 of 18 US 2015/0072349 A1 FIGURE 6 CA9-9 LAMC2 PCOOOO1 - X 8 - A. P-OOOO X w y t Healthy Benign Cancer DSG2 p=0.023 Patent Application Publication Mar. 12, 2015 Sheet 8 of 18 US 2015/0072349 A1 FIGURE 7A ROC (Healthy vs Cancer) C 9 d OO C &S to 2. > C C) O) o w - DSG2 (AUC=O.801) S LAMC2 (AUC=0.866) - - CA199 (AUC=0.816) C 100 80 60 40 20 O Specificity (%) Patent Application Publication Mar. 12, 2015 Sheet 9 of 18 US 2015/0072349 A1 FIGURE 7B ROC (Benign vs Cancer) o 9 d o d SS to > i CO c w - DSG2 (AUC=0.645) o LAMC2 (AUC=0.787) N - - CA199 (AUC=0.827) o 100 8O 60 40 2O O Specificity (%) Patent Application Publication Mar. 12, 2015 Sheet 10 of 18 US 2015/0072349 A1 FGURE 8A i) p40 0001 ii) p40 0001 --p=0.3098 rp20-4553 86 - 88- r- 10000 - 66 4. pk0 0001 46 w 6 --- 2 s 2000 * - Se is 9. 20 this set syst wns st 3 4 5 FIGURE 8B; 0.8 2 t s 0.4 0.2- - CUZOl ACs0.79 (0.71-86) - - - A199 AUc=0.82 (0.75-0.38) cuzo-CA19.9, AUC=0.86 (0.80-092) Q0 ---------------- 0.0 0.2 0.4 0.8 0.8 0. - Specificity Patent Application Publication Mar. 12, 2015 Sheet 11 of 18 US 2015/0072349 A1 FIGURE 9A i) ii) p:00009 p=0.065 s re 90 O pro SS s si----- is 70 50 600 s: a 30 ... -- wa So 2000 s s gs 6 3 2 Healthy Benign Stage B Stage V Healthy Benign Stage 18 Stage IV OAC PAC FIGURE 9B. 10 0.8 0.6 04 0.2 a- CA99, AUC=O,81 (0.70-0.92) - - - CUAD, AUC=O.79 (0.67-0.90) CUZD1+CA99, AUC=0.84 (0.75-0.94 0.0 ----- 0.0 0.2 0.4 0.6 0.8 1- Specificity Patent Application Publication Mar. 12, 2015 Sheet 12 of 18 US 2015/0072349 A1 FIGURE 10 suuuu A. r-Trn- s p=0.002 pK.900" p<0.0001 - PTrl p:0.007 70 - p40.0001 8S - g 50 1,6 60 s0.08 - 45 . " r 23 -it- 25 s S is a 2. O. p<0.0001 - - t- - - - E -TR) -- F 2002 p=0.004 p:00 =0C2 ps:0.002 pro.2 P p=0.8 :a. 13:o 1 , . - 50 w v. Patent Application Publication Mar. 12, 2015 Sheet 15 of 18 US 2015/0072349 A1 FIGURE 11E 1.O. 0.8 0.6 e e 2 8 0.4 0.2 - CA19-9, AUC=0.76 (0.68-084) --- CUZD1 AUC=0.77 (0.69-084) LAMC2, AUC=0.71 (0.62-0.79) 0.0 00 0.2 0.4 0.6 0.8 10 1 - Specificity FIGURE 11F 10 0.8 0.6 % 0.4 0.2 - CA19-9, AUC=0.76 (0.68-084) -a-- CA19-9+CUZOl, AUC=0.84 (0.77-090) CA19.9+LAMC2, AUC=0.8l (0.74–0.88) CA199+CUZOl+LAMC2, AUC=0.87 (0.81-093) 0. 0.0 0.2 0.4 0.6 0.8 O 1 - Specificity Patent Application Publication Mar. 12, 2015 Sheet 16 of 18 US 2015/0072349 A1 FIGURE 11G 1.0 0.8 0.6 2 W O.4 0.2 - CA19-9, AUC=0.81 (0.77–086) : --- CUZD1, AJC=0.74 (0.69-0.80) on LAMC2, AJC=0.75 (0.69-080) 0.0 - ----- O.O 0.2 0.4 0.6 0.8 10 1 - Specificity FIGURE 11H 10 O.8 s 0.6 t s i. g '. V : O4 0.2 a- CA19-9, AUC=0.8l (0.77-0.86) -- a CA199+CUZD, AUC= 0.87 (0.84-0.91) CA199+LAMC2, AUC=0.86 (0.83-0.90) 0.0 0.2 0.4 0.6 0.8 O 1 - Specificity Patent Application Publication Mar. 12, 2015 Sheet 17 of 18 US 2015/0072349 A1 FIGURE 12A Specificity Sensitivity CA19-9., CUZD1 - - - - - - - ... * * (37IU/ml). (2.2ng/ml). ng/ml). - Benign (N=130) 83% (108/130) Resectable Cancers (N=51) 49% (25/51) 53% (27/51) Maybe Resectable Cancers (N=150) 74% (111/150) 54% (81/150) 59% (88/150) Non-Resectable Cancers (N=49) 80% (39/49) 80% (39/59) 55% (27/49). Cutoffs: Ca19.9- 37 IU/m CUZD1 = 2.2 ng/ml LAMC2= 176 ng/ml FIGURE 12B Specificity/Sensitivit CA19.9 (37 CA19.9 - CUZD1 + ... IU/ml) CA19.9 +CUZD1 CA19.9 + LAMC2 LAMC2 Benign (N=130) 83% (108/130) 75% (97/130) 77% (100/130) 72% (93/130) Resectable Cancers (N=51) 49% (25/51) 69% (35/51) 61% (31/511), 76% (39/51) Maybe Resectable Cancers (N=150) 74% (111/150) 83% (125/150) 83% (124/150) 89% (133/150) Non-Resectable Cancers (N=49) 80% (39/49). 94% (47/59) 82% (40/49) 94% (46/49) Cutoffs: Ca19.9- 37 U/ml CUZD1 = 3 ng/ml LAMC2= 293 ng/ml An example of optimized cutoffs for combination of markers: Cutoffs: Ca19.9= 58 IU/m CUZD1 = 3.6 ng/ml LAMC2= 410 ng/ml Patent Application Publication Mar. 12, 2015 Sheet 18 of 18 US 2015/0072349 A1 FIGURE 3: CA199 & CUZD1 (at same specificity) | soivri -: ufu OZho US 2015/0072349 A1 Mar. 12, 2015 CANCER BOMARKERS AND METHODS OF cancer, wherein the cancer is pancreas cancerif CUZD1, USE LAMC2, AQP8, CELA2B, CELA3B, CTRB1, CTRB2, GCG, IAPP, INS, KLK1, PNLIPRP1, PNLIPRP2, PPY, RELATED APPLICATIONS PRSS3, REG3G, SLC30A8, DSP GP73 and/or DSG2 is 0001.