US 20200078401A1 IN ( 19 ) United States (12 ) Patent Application Publication ( 10) Pub . No .: US 2020/0078401 A1 VIJAYANAND et al. (43 ) Pub . Date : Mar. 12 , 2020 (54 ) COMPOSITIONS FOR CANCER (52 ) U.S. CI. TREATMENT AND METHODS AND USES CPC A61K 35/17 ( 2013.01) ; A61K 45/06 FOR CANCER TREATMENT AND ( 2013.01 ) ; C120 1/6886 ( 2013.01 ) ; A61P PROGNOSIS 35/00 (2018.01 ) ( 71 ) Applicants : La Jolla Institute for Allergy and Immunology , La Jolla , CA (US ) ; UNIVERSITY OF SOUTHAMPTON , (57 ) ABSTRACT Hampshire (GB ) (72 ) Inventors : Pandurangan VIJAYANAND , La Jolla , CA (US ) ; Christian Global transcriptional profiling of CTLs in tumors and OTTENSMEIER , Hampshire (GB ) ; adjacent non -tumor tissue from treatment- naive patients Anusha PreethiGANESAN , La Jolla , with early stage lung cancer revealed molecular features CA (US ) ; James CLARKE , Hampshire associated with robustness of anti - tumor immune responses . (GB ) ; Tilman SANCHEZ - ELSNER , Major differences in the transcriptional program of tumor Hampshire (GB ) infiltrating CTLswere observed that are shared across tumor subtypes . Pathway analysis revealed enrichment of genes in ( 21 ) Appl. No .: 16 / 465,983 cell cycle , T cell receptor ( TCR ) activation and co -stimula tion pathways , indicating tumor- driven expansion of pre ( 22 ) PCT Filed : Dec. 7 , 2017 sumed tumor antigen - specific CTLs. Marked heterogeneity in the expression ofmolecules associated with TCR activa ( 86 ) PCT No .: PCT /US2017 / 065197 tion and immune checkpoints such as 4-1BB , PD1, TIM3, $ 371 ( c ) ( 1 ) , was also observed and their expression was positively ( 2 ) Date : May 31 , 2019 correlated with the density of tumor- infiltrating CTLs. Tran scripts linked to tissue- resident memory cells ( TRM ), such Related U.S. Application Data as CD 103 , were enriched in tumors containing a high (60 ) Provisional application No.62 / 431,265 , filed on Dec. density of CTLs, and CTLS from CD 103 high tumors dis 7 , 2016 , provisional application No. 62 /522,048 , filed played features of enhanced cytotoxicity , implying better anti- tumor activity . In an independent cohort of 689 lung on Jun . 19 , 2017 . cancer patients , patients with CD103 high (TRM rich ) tumors Publication Classification survived significantly longer. In summary , the molecular ( 51 ) Int . Cl. fingerprint of tumor- infiltrating CTLs at the site of primary A61K 35/17 ( 2006.01 ) tumor was defined and a number of novel targets identified A61P 35/00 ( 2006.01) that appear to be important in modulating the magnitude and C12Q 1/6886 ( 2006.01 ) specificity of anti -tumor immune responses in lung cancer . Exhaustion signature (up genes ) Exhaustion signature ( down genes ) Lung cancer T cell signature (up genes ) Anergy signature (up genes ) Senescence signature (up genes ) 0 4 P0.04 0.2 P = 0.02 P = 0.02 0.4 P0.38 P = 018 q = 0.11 0.5 0.2 0 = 0.11 q = 0.03 q = 0 : 23 RES 0 . RES -0.2 RES -0.4 -0.4 1 10 10 Metric Metric Metric Metric 10 Metric -10 5 5 20 " 10 5 20 Variable index (x1000 ) Patent Application Publication Mar. 12 , 2020 Sheet 1 of 17 US 2020/0078401 A1 P0.18 0.23q= 20 Senescencesignature(upgenes) 15 10 6 0.4 RES -0.4Ò Metric -10 20 P-0.38 0.38=q 15 10 5 0.4 RES -0.4 Metric-10 20" P=0.02 0.03=q Exhaustionsignature(downgenes)LungcancerTcellsignatureupgenesAnergysignature(genes) 15' 10' Fig.1 5 0.5 RES -0.5 Metric-10 P.0.02 0.11=q ------------ 20" 15" 10' 5 ha 0.2 -0.2 0.4 10 RES Metric P=0.04 0.11=Q Exhaustionsignature(upgenes) 10*15520 Variableindex(x1000) 10 0.4 0.2 .-10 -0.2 Metric Patent Application Publication Mar. 12 , 2020 Sheet 2 of 17 US 2020/0078401 A1 -Log (Pvalue ) 2.5 7.5 5.0 -Log(Pvalue) 52 Upregulated Downregulated 70 47 lymphocytesinsignaling CD27 187 signalingINOS 87 junctionneuromuscular atinteractions Agrin 14 activationvirusesincell activation stellate NFB& fibrosis Hepatic 25225315 synthesisnovo de ATMP 40 RAsignalingincells cytokineendothelial IL6 in&kinases fibroblasts JAK ,Macrophages 247 38 signalingfactormetastasis activating cancer cellColorectal B 55 72 compoundssignalingmediated phosphate APRIL inositol ot pathway Super controlcycle cell in proteins CHK of Role 154117197 Signalingdifferentiationp53 Thelper 2A.Fig 27402 metabolismphosphate myoinositol -D signalingsynthesisAphosphoinositidekinase Protein -3 135 153 replication)chromosoma ofcontrol cycle Cell synthesistetrakisphosphate )3,4,5,8 (myoinositol -D 88 synthesisdegradationtetrakisphosphate phosphoinositide )1,4,5,8-3 (myoinositol -D 66 lymphocytesinsignaling 4-1BB RAinsignaling cell B& T Altered 78 KinaseLike -Polo of roles Mitotic 144238 HBCSregulationresponse checkpointdamage DNA damage inBRCA1 DNA of MRole/G2 : cycle Cell 59 RAinosteoclast ,Osteoblast 100 signalingATM Percent Patent Application Publication Mar. 12 , 2020 Sheet 3 of 17 US 2020/0078401 A1 JUNJUN 2kb Chr1 20.5 20.51 14 12 Polo-LikeKinase(9) ATMsignaling(13) 49.6kb Mitoticrolesof 4 P53signaling(9) Chr12 81 INFRSF9CD2 10.8, 10.8 12 10 ... www 7,3kb regulation(8) Chr114-1BB) cycle:G2/MDNACell damagecheckpoint FIG.2B 4.6 12 9 FIG.2C 68kb response10)( CCNB1 Chr5 0.6 3 RoleofBRCA1in 0.6 control(6) cancersignaling(14) DNAdamage RoleofCHKproteinsIncellcyclecheckpoint 4 Hereditarybreast PLK1 wwwwwwwww 7.3kb Chr16 0.4 0.47 ) RPKM ( ) normalized( Expression RNA Expression Patent Application Publication Mar. 12 , 2020 Sheet 4 of 17 US 2020/0078401 A1 NSOLOTIL Ligand Transmembrane receptor Transporter EnzymeTranscriptiora Mregulator Kinase Complex Upregulated TRAF5 Y V00271 CD27 ATRAF2 MEKK 45.3 SNIK InducedCell Death TRAF2 OIKK NFB TILLungN- psa FIG.2E 4-1BBL 4-1BB JASK1 MAPK INK Cytotoxicity FIG.2D TRAFI MEK1/2 oo ERKTA2UNK ASIAN extracellular space Cytoplasm CORNER Nucleus Proliferation PBMC 010 .. Patent Application Publication Mar. 12 , 2020 Sheet 5 of 17 US 2020/0078401 A1 left()UNTIL TILONcenter() Tilhigh(right) N-TL TILDW TILNgh TIGIT 7.3kb Chr3 11,7 11,7 117 13 12 11 10 LungTIL.N- NSCLCTIL 2.6kb LAG3Chr12 REG 901 9.1 9.1 13 12 11 (TIM3)HAVCR2 10.2kb Fig.3 2FFig. Chr5 5 Frequentclonotypes ???????? 11.7kb (4-1BB) ?????????????? TNFASFOOhi 62 62 62 12 10 8 clonotypes of Number PDCD1 3.9kb Chr2 ) RPKM( ) normalized( Expression RNA Expression Patent Application Publication Mar. 12 , 2020 Sheet 6 of 17 US 2020/0078401 A1 highTIL N-TIL TLbW STK38 23.5kb Chr6 8 2.2 2.2 2.2 11 10 KLF2 1.1kb honde 9 Chr19 17,3 13 TILhigh(right) S1PA1 2.0kb Chr1 4AFig. 13.7 13.7 14 10 N-TILleft()ATILIWcenter) CXOR 2.1Kb Chr3 4 23.7 23.7 23.7 13 12 10 ITCAE onhimpunan ..... 37.2kb Chr17 8 6.6 6.6 12 ) RPKM( )normalized ( Expression ANA Expression Patent Application Publication Mar. 12 , 2020 Sheet 7 of 17 US 2020/0078401 A1 31.5 26:3 28 OD103 NSCLCTIL 49.6 1.6 65.8 1.5 66 43.5 5.9 PD1 LungTILN- FIG.4B 1.3 918 1.2 FIG.40 0.7 44.8 0.05 0:1 CD8a PBM 54.2 1.35 97.2 CD103 0.8 97.7 CD103 CD103 CD8 PD1 4-1BB TILlowNSCLC NSCLChighTIL Patent Application Publication Mar. 12 , 2020 Sheet 8 of 17 US 2020/0078401 A1 SA 31.3 P<0.001 0.005=q 1520 Variableindex(x1000) CD49a TRM(downgenes) 5 CD69 COR7 31.7 0 0.2 -0.2 10 RES Metric SEN FIG.4D FIG.4E 1612 CD49a 12900 0.56P= 0.55q= 31.1 2.2 286 TAM(upgenes) 1551020 Variableindex(x1000) 28.6 CD103 CD69 KLRG1 CD103 nown 0.4 0.2 0.2 -0.4 -10 RES Metric Patent Application Publication Mar. 12 , 2020 Sheet 9 of 17 US 2020/0078401 A1 CD103low(center) CD103high(right) N-TIL(left) TILN- CD10310 CD103high Upregulated(all) 4.8kb Chir17BIRC5 BROW 73.7 Cytokine Enzyme TranscriptionalRegulator Phosphatase Peptidase Other 1.1 1.1 1.1 10 NSOLCIIL kb8.5 GBP4 GBP5 OUT 0.2 421.4 GBP2 Chr15CCNB2 GBP1 COWOTCH1 80453* 1.1 10 0.2 2016 ... PARPO TILhungN- SCD38 HOW 7.5kb FIG.5A FIG.5B CCL5 FIG.4F AURKBChr17 10.7 78.5 BCDIPSMB 0.9 09 COLBY their Internet 1.8kb BST20 PSMBS CDC20 ........ PBMC UBE2L62 PSMEZ? Chr1 1.2 1.2 10 12.2 192.6 STATZCO STATU SEC11A RARRES K167 CD103 18.5kb 18 ACC Chr14.DLGAPS 0.8 0.8 ) RPKM( ) normalized( Expression Expression Patent Application Publication Mar. 12 , 2020 Sheet 10 of 17 US 2020/0078401 A1 P0.036= CDShightumors CD103high 200030004000 LCD1036 Days FIG.5G CD103low(center) CD103high(right) 1000 IN-TIL(left) 80 40 20 0 332 100 30.7 46.3 206 survival Percent IFNG SC 14 A Granzyme P=0.043 4000 ) normalized( .IFNY Expression IFNG 396 224 20.4 CD103high CD103low 3000 2000 Days FIG.5F GZMA FIG.5D FIG.5C 13.9 22.6 9.8 S 1000 B Granzyme 103CD ) nomalized( Expression GZMA 100 80. 60 40 20 CD103low CD103high survival Percent CD8*TILS GZMB 33.8 Perforin CD103 P=0.086 4000 ) nomalized( GZMB of MFI Expression GZMB highCD CD8low 3000 2000 Days FIG.5E 1000 100 80 60 40 20 survival Percent Patent Application Publication Mar. 12 , 2020 Sheet 11 of 17 US 2020/0078401 A1 CD103center() high(right)CD103 N-TIL(left) CD8+CD103TILS-left() CDB+CD103*Tiloright() RBPJ 15 - URC TUUT + CD39 of % 12 . NABI P2RX7 100 + CD38 of % 12 6 N BATF SIRPG FIG.6A 29.01 FIG.6B 8 CD39 29,9 10,5 7.5. KIR2DL4 CD39 2 CD38 ) namalized( expression 5.5. 0.5. CD38 ) Expressionnormalized( 59.8 35.2 KIA2DL4 CD103 Patent Application Publication Mar. 12 , 2020 Sheet 12 of 17 US 2020/0078401 A1 S100A10 6X3071 w S1PRI Reducedcellmovement G-proteincoupledreceptor Peptidase Downregulated Cytokine Other FIG.7A CAST TIMP7 0 TNF Patent Application Publication Mar.