#METABOLOMICS WORKBENCH juliehaines_20230221_084725 DATATRACK_ID:3753 STUDY_ID:ST002487 ANALYSIS_ID:AN004061 PROJECT_ID:PR001607 VERSION 1 CREATED_ON February 21, 2023, 9:03 am #PROJECT PR:PROJECT_TITLE Simultaneous targeting of PD-1 and IL2Rβγ with radiation therapy to inhibit PR:PROJECT_TITLE pancreatic cancer growth and metastasis PR:PROJECT_SUMMARY In pancreatic ductal adenocarcinoma (PDAC) patients, we show that response to PR:PROJECT_SUMMARY radiation therapy (RT) is characterized by increased IL2Rβ and IL2Rγ and PR:PROJECT_SUMMARY decreased ILR2α expression. The bispecific aPD1-IL2v is a PD-1-targeted IL-2 PR:PROJECT_SUMMARY variant (IL2v) immunocytokine with engineered IL-2 cis-targeted to PD-1 and PR:PROJECT_SUMMARY abolished IL2Rα binding, which enhances tumor-antigen specific T cell PR:PROJECT_SUMMARY activation while reducing regulatory T cell (Treg) suppression. Using aPD1-IL2v PR:PROJECT_SUMMARY in orthotopic PDAC KPC-driven tumor models, we show marked improvement in local PR:PROJECT_SUMMARY and metastatic survival along with profound increase in tumor-infiltrating PR:PROJECT_SUMMARY polyfunctional CD8+ T cell subsets with a transcriptionally and metabolically PR:PROJECT_SUMMARY active phenotype, and preferential activation of antigen-specific CD8+ T cells. PR:PROJECT_SUMMARY In combination with single dose RT, aPD1-IL2v treatment results in a robust, PR:PROJECT_SUMMARY durable expansion of polyfunctional CD8+ T cells, T cell stemness, PR:PROJECT_SUMMARY tumor-specific memory immune response, natural killer (NK) cell activation, and PR:PROJECT_SUMMARY decreased Tregs. These data show that aPD1-IL2v leads to profound local and PR:PROJECT_SUMMARY distant response in PDAC. PR:INSTITUTE University of Colorado Denver PR:LABORATORY Lab of Angelo D'Alessandro in collaboration with lab of Sana Karam PR:LAST_NAME Haines PR:FIRST_NAME Julie PR:ADDRESS 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA PR:EMAIL julie.haines@cuanschutz.edu PR:PHONE 3037243339 #STUDY ST:STUDY_TITLE Simultaneous targeting of PD-1 and IL2Rβγ with radiation therapy to inhibit ST:STUDY_TITLE pancreatic cancer growth and metastasis - mouse spleen and lymph node T-cell ST:STUDY_TITLE metabolomics ST:STUDY_SUMMARY Mice were orthotopically implanted with PK5L1940 cells then radiation therapy (8 ST:STUDY_SUMMARY Gy) administered 7 days post-implantation. PD1-IL2v and aCD25 dosed once per ST:STUDY_SUMMARY week beginning day 7 post-implantation. Spleen and associated lymph nodes were ST:STUDY_SUMMARY collected at time of sacrifice and sorted for CD8+ T-cells. The obtained T-cells ST:STUDY_SUMMARY were profiled by mass spectrometry-based metabolomics. ST:INSTITUTE University of Colorado Denver ST:LAST_NAME Haines ST:FIRST_NAME Julie ST:ADDRESS 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA ST:EMAIL julie.haines@cuanschutz.edu ST:PHONE 3037243339 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - MSL-1 factor:Untrx RAW_FILE_NAME=AG-23-MSL-1-r4 SUBJECT_SAMPLE_FACTORS - MSL-2 factor:Untrx RAW_FILE_NAME=AG-23-MSL-2-r5 SUBJECT_SAMPLE_FACTORS - MSL-3 factor:Untrx RAW_FILE_NAME=AG-23-MSL-3-r6 SUBJECT_SAMPLE_FACTORS - MSL-4 factor:RT RAW_FILE_NAME=AG-23-MSL-4-r13 SUBJECT_SAMPLE_FACTORS - MSL-5 factor:RT RAW_FILE_NAME=AG-23-MSL-5-r9 SUBJECT_SAMPLE_FACTORS - MSL-6 factor:RT RAW_FILE_NAME=AG-23-MSL-6-r7 SUBJECT_SAMPLE_FACTORS - MSL-7 factor:IL2v RAW_FILE_NAME=AG-23-MSL-7-r12 SUBJECT_SAMPLE_FACTORS - MSL-8 factor:IL2v RAW_FILE_NAME=AG-23-MSL-8-r15 SUBJECT_SAMPLE_FACTORS - MSL-9 factor:IL2v RAW_FILE_NAME=AG-23-MSL-9-r14 SUBJECT_SAMPLE_FACTORS - MSL-10 factor:RT+IL2v RAW_FILE_NAME=AG-23-MSL-10-r1 SUBJECT_SAMPLE_FACTORS - MSL-11 factor:RT+IL2v RAW_FILE_NAME=AG-23-MSL-11-r8 SUBJECT_SAMPLE_FACTORS - MSL-12 factor:RT+IL2v RAW_FILE_NAME=AG-23-MSL-12-r11 SUBJECT_SAMPLE_FACTORS - MSL-13 factor:aCD25 RAW_FILE_NAME=AG-23-MSL-13-r10 SUBJECT_SAMPLE_FACTORS - MSL-14 factor:aCD25 RAW_FILE_NAME=AG-23-MSL-14-r3 SUBJECT_SAMPLE_FACTORS - MSL-15 factor:aCD25 RAW_FILE_NAME=AG-23-MSL-15-r2 #COLLECTION CO:COLLECTION_SUMMARY Spleens of C57BL/6 mice were homogenized to a single cell suspension by mashing CO:COLLECTION_SUMMARY the spleen through a 70 uM cell strainer, and the erythrocytes were lysed with CO:COLLECTION_SUMMARY ACK (ammonium-chloride-potassium) lysis buffer for 3 min at RT. CD8 T cells were CO:COLLECTION_SUMMARY sorted with a CD8-negative selection Stemcell isolation kit following CO:COLLECTION_SUMMARY manufacturer instructions. Cells were washed with PBS at 1200RPM, 4degC for 10 CO:COLLECTION_SUMMARY minutes and pellets were flash frozen. CO:SAMPLE_TYPE Spleen; T-cells #TREATMENT TR:TREATMENT_SUMMARY Mice were orthotopically implanted with PK5L1940 cells. RT administered 7 days TR:TREATMENT_SUMMARY post-implantation. PD1-IL2v and aCD25 dosed once per week beginning day 7 TR:TREATMENT_SUMMARY post-implantation. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Metabolites from frozen T-cell pellets were extracted with cold 5:3:2 SP:SAMPLEPREP_SUMMARY MeOH:acetonitrile:water at a concentration of 4 million cells/mL. Samples were SP:SAMPLEPREP_SUMMARY vortexed 30 min at 4 degrees C then supernatants clarified by centrifugation (10 SP:SAMPLEPREP_SUMMARY min, 10,000 g, 4 degrees C) and transferred to autosampler vials. SP:PROCESSING_STORAGE_CONDITIONS 4℃ SP:EXTRACT_STORAGE -80℃ #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Positive C18 CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Phenomenex Kinetex C18 2.1 x 150 mm, 1.7 um CH:SOLVENT_A 100% water 0.1% formic acid CH:SOLVENT_B 100% acetonitrile 0.1% formic acid CH:FLOW_GRADIENT 0-0.5 min 5% B, 0.5-1.1 min 5-95% B, 1.1-2.75 min hold at 95% B, 2.75-3 min CH:FLOW_GRADIENT 95-5% B, 3-5 min hold at 5% B CH:FLOW_RATE 450 uL/min CH:COLUMN_TEMPERATURE 45 CH:SAMPLE_INJECTION 10 uL #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Orbitrap Exploris 480 MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS We use a Thermo Orbitrap Exploris 120 (not available in the drop down box). MS:MS_COMMENTS Resolution 120,000, scan range 65-975 m/z, maximum injection time 100 ms, MS:MS_COMMENTS microscans 1, automatic gain control (AGC) detection duration 20 msec, source MS:MS_COMMENTS voltage 3.5 kV, capillary temperature 320 C, vaporizer temp 200 C, and sheath MS:MS_COMMENTS gas 50, auxiliary gas 10, and sweep gas 1 (all nitrogen). Data converted to MS:MS_COMMENTS mzXML using RawConverter. Metabolites were annotated and integrated using Maven MS:MS_COMMENTS in conjunction with the KEGG database. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS peak area MS_METABOLITE_DATA_START Samples MSL-1 MSL-2 MSL-3 MSL-4 MSL-5 MSL-6 MSL-7 MSL-8 MSL-9 MSL-10 MSL-11 MSL-12 MSL-13 MSL-14 MSL-15 Factors factor:Untrx factor:Untrx factor:Untrx factor:RT factor:RT factor:RT factor:IL2v factor:IL2v factor:IL2v factor:RT+IL2v factor:RT+IL2v factor:RT+IL2v factor:aCD25 factor:aCD25 factor:aCD25 L-alanine 6220456 117104 67206 232560 209320 136396 1903167 203713 758283 372548 161126 568129 72993 307703 41451 L-arginine 2886038 191098 457760 341649 1918120 624038 2583023 896678 1808375 1585220 1158713 2625003 346805 1450789 289284 L-asparagine 794468 4887 3822 7360 14597 6429 302934 11431 71365 34281 19935 47180 1106 19273 0 L-aspartate 3201557 75990 105104 55061 274961 46707 1857177 295597 774993 476964 202489 502550 218718 282114 96994 L-glutamate 7578056 214302 192026 325565 608511 169620 3559566 451774 1501267 778142 366914 835883 166203 526636 229258 L-glutamine 1612133 272552 19963 229407 45368 84006 471571 49128 136689 68894 29231 83019 8462 116132 11504 glycine 1239623 10735 23514 20886 65159 21283 718253 90323 236076 154441 69852 172582 43856 73421 13812 L-histidine 710123 49858 20481 65561 42014 43961 165468 11304 58459 24712 17074 82709 11444 25335 9395 L-leucine/isoleucine 10456415 325719 183455 769155 1159944 394607 3938987 556164 1665555 783760 498344 1547486 136166 902696 217865 L-lysine 2702733 35898 88980 73284 477946 114755 690459 120055 246987 218934 227769 382202 65169 222843 116629 L-methionine 6181472 34928 53995 80290 420220 94438 1910100 272219 998755 412832 200108 720949 70971 415375 64399 L-phenylalanine 2734763 65302 123115 106958 825918 126174 820303 179280 421134 299674 287310 506307 57061 277735 211003 L-serine 1555051 31735 10217 50684 33883 10585 662047 16396 154625 71373 27721 103289 14675 38132 4371 L-threonine 2453774 50177 23451 77141 71923 49482 1057199 86094 282792 131270 56025 251214 17327 105852 6806 L-tryptophan 5338840 209066 589131 304742 1577107 642589 1146148 448310 754948 1034001 912880 1949160 210137 597696 555969 L-tyrosine 6320108 154481 100482 326924 461403 171455 1934298 424388 1079202 786238 320510 1122202 98129 439945 152537 L-valine 13710311 4825861 4195560 4782457 9913964 5772354 7666969 3873959 7077381 4421966 2255006 5793172 2057224 3259788 1341740 AMP 10700347 99837 2739896 97465 7348932 718935 13191443 9205981 12274212 11914684 5128408 7972368 2445888 7013712 2420616 Guanine 164776 10241 12803 10933 92813 21997 92410 65223 55080 57569 39841 57455 14407 55591 14406 CMP 1918860 1266 49836 1762 492682 141943 419078 126255 396420 194970 92704 518185 27046 222424 46817 UMP 632148 1931 162664 1485 481348 57163 455029 331798 518187 389670 336882 279722 154116 347368 141874 Uracil 546748 10427 9495 12574 43464 18339 178662 18524 58313 32503 31239 91682 16334 23042 8594 ADP-D-ribose 8725 6361 44651 1427 159220 14842 18214 25685 7916 21167 27333 1845 36105 56191 60729 Maltotriose 18461 58721 91332 89442 107517 94869 54092 47669 14584 283876 267863 275127 96758 37714 116567 Glutathione 25936742 295919 1557647 76250 5976130 409371 13584976 4631759 6874351 6103348 2770444 5555686 1548026 2952192 1515883 Glutathione disulfide 819488 1314 25503 4266 87725 49337 175618 3538 54348 14999 27042 69966 4056 10020 17786 5-Oxoproline 864420 248684 78470 156055 103808 152843 386431 111698 174597 97140 87319 338064 160492 139449 64060 Cys-Gly 172276 0 18621 0 42660 0 92242 32032 35564 36951 39356 38235 22017 78742 18518 gamma-L-Glutamyl-L-cysteine 101064 1947 2314 1197 12832 3784 36884 6082 12950 13148 9365 16958 2960 13600 2336 gamma-L-Glutamyl-D-alanine 68365 6207 0 15465 11875 3417 69745 3925 20235 1833 1745 5044 2358 9357 0 gamma-Glutamyl-gamma-aminobutyrate 32799 1843 2617 6247 23527 2481 33607 5286 24145 2459 7406 4458 3528 28695 0 10-Formyldihydrofolate 33446 0 5755 0 24993 3699 43005 18834 25791 17863 34891 38656 5741 16730 15798 Ornithine 72527 7496 17369 9681 24394 7188 12338 1443 4630 5240 3567 18672 7301 3172 9824 L-Citrulline 71805 116296 5764 75652 7645 26904 31722 2964 4844 3037 0 12423 3401 6589 0 Putrescine 65125 3976 55086 1536 176011 28470 16464 61509 34676 58260 120947 89124 28207 39694 93300 Spermidine 1678123 101493 3449256 50392 7571528 592068 387369 1210908 1037935 2193801 4989668 4177795 1292035 1814572 5471986 Spermine 395696 34565 1837914 25263 3708287 234403 468818 423136 320794 799525 2301906 1535596 473717 1049849 3661926 Carnosine 76086 4703 0 9864 19706 7406 20225 6442 16107 10427 8290 7759 1160 15639 1470 N-Acetylornithine 485634 87036 18035 226339 99273 33056 261698 55002 134758 86873 45569 47613 73454 174496 6317 Guanidinoacetate 514437 1690 0 2845 21864 11225 91144 5008 35875 3719 5228 31087 4754 19433 0 trans-4-Hydroxy-L-proline 296829 50405 28692 58541 132154 46562 79560 31271 45941 29514 23501 59746 21121 56635 20703 Taurine 4179572 58473 153904 57283 632251 128955 2657180 294083 932138 578610 342335 726023 139303 468962 145604 L-Methionine S-oxide 42586 36921 4477 47101 25952 29767 51760 21268 65342 32172 25323 44684 17552 49804 12576 Indole-3-acetate 1862356 1352 102274 3528 552926 24980 464950 142965 250177 353619 396630 600074 39330 181878 81010 Anthranilate 45764 30018 15725 24792 20862 39388 33838 13269 19385 20588 0 25345 18767 10219 0 Picolinic acid 26066 6539 36425 4784 24619 11315 4502 5470 5830 11672 9122 8923 6732 7250 8330 g-Oxalo-crotonate 2040444 18681 79044 0 424181 271208 717557 553059 1127992 772723 286535 1033103 80421 770462 82549 N-Methylethanolamine phosphate 339496 238225 208007 280593 169994 213602 874780 273381 280617 286798 161104 231348 233869 239588 222772 Sphingosine 2996104 93350 550392 153366 3386221 1115003 790542 552892 883834 787194 677675 855680 282901 911272 919344 Acetylcholine 1817530 292094 517329 250382 1565366 309270 340270 431102 741627 704957 540062 895015 350734 461857 488864 Choline 44515244 1664388 8246107 2188391 27507486 3933377 18283918 6206096 11012769 15138040 7945600 14634781 4736158 13159501 11822199 L-Carnitine 30765662 1248290 15328896 1277171 22845830 5773059 16198273 11548604 9020677 15621211 18000486 26093726 11066147 18237600 11592936 acetyl-carnitine (acyl-C2) 64434868 1653252 16912392 996891 65644676 6980929 22774702 21259736 28204048 39669068 16935490 24381576 14787145 14972725 26796010 propionyl-carnitine (acyl-C3) 1823762 360612 1288071 219465 3068189 766958 978207 2938107 1532250 2496132 1877634 1028233 1470381 1501436 1900977 butanoyl-l-carnitine (acyl-C4) 50558 31024 62135 44847 176102 63110 29541 83860 49989 92887 74013 66513 35399 43936 113227 acyl-C4-OH 2198011 32822 233798 24148 1370427 174000 720620 390314 794811 885264 485270 767747 205907 375726 273308 acyl-C4-DC 188302 17732 22835 20810 79163 17438 70250 19978 55440 26869 22182 78627 26502 36047 15398 acyl-C5-OH 629968 30071 78502 13857 222964 48903 234977 117041 193734 184654 140037 259923 61189 165620 43195 hexanoyl-L-carnitine (acyl-C6) 56193 12491 49457 40904 291625 49962 9855 102202 28361 78459 20798 35739 50355 15232 110096 O-dodecanoyl-carnitine (acyl-C12) 16572 3976 7772 7838 59532 9629 4131 26194 4122 31417 6527 12037 3782 8979 26979 O-dodecenoyl-carnitine (acyl-C12:1) 178914 53096 162160 56154 154149 83753 115072 60131 101296 79244 156307 85157 96599 101879 143844 O-tetradecanoyl-L-carnitine (acyl-C14) 144131 14313 28495 29216 577987 71406 58668 164488 77942 308991 50975 112674 30139 37128 154740 L-Palmitoylcarnitine (acyl-C16) 1766257 118443 287387 195227 3545765 586251 867254 1141258 768976 1803094 534174 1205293 397342 535598 1057393 Hexadecenoyl-carnitine (acyl-C16:1) 53267 6938 21174 28196 147362 22007 18432 24909 17563 84090 22849 40979 11621 15815 56505 Octadecanoyl-L-carnitine (acyl-C18) 2652059 128253 459818 148321 2454936 429762 1131003 985134 752297 832549 421413 591324 462349 781986 1004567 O-octadecenoyl-L-carnitine (acyl-C18:1) 340129 53893 99512 171767 1072412 110873 157670 232997 139559 496867 94745 245679 80597 94881 335247 acyl-C18:2 (Linoleoyl-CoA) 107107 4594 17457 24069 239894 26554 47032 46502 23441 120516 23699 55240 14512 12998 88419 acyl-C20:4 276047 0 19967 4854 174693 37488 59063 88741 47097 66891 20453 72864 14331 32599 49393 Biliverdin 11614 59712 138136 74005 221900 127071 6828 56045 25003 428237 233295 159559 104936 39486 201366 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name KEGG ID parent medRt L-alanine C00041 90.0545 0.6650 L-arginine C00062 175.1177 0.6390 L-asparagine C00152 133.0600 0.6550 L-aspartate C00049 134.0440 0.6580 L-glutamate C00025 148.0595 0.6610 L-glutamine C00064 147.0756 0.6780 glycine C00037 76.0388 0.6570 L-histidine C00135 156.0758 0.6180 L-leucine/isoleucine C00123 132.1011 0.7450 L-lysine C00047 147.1119 0.6040 L-methionine C00073 150.0573 0.7140 L-phenylalanine C00079 166.0852 1.0900 L-serine C00065 106.0493 0.6610 L-threonine C00188 120.0648 0.6880 L-tryptophan C00078 205.0958 1.7710 L-tyrosine C00082 182.0800 0.7260 L-valine C00183 118.0856 0.6730 AMP C00020 348.06842 0.688 Guanine C00242 152.055725 0.717 CMP C00055 324.057129 0.688 UMP C00105 325.041046 0.711 Uracil C00106 113.033951 0.714 ADP-D-ribose C01882 560.075012 0.808 Maltotriose C01835 505.177979 2.182 Glutathione C00051 308.089325 0.699 Glutathione disulfide C00127 613.156677 0.712 5-Oxoproline C01879 130.049088 0.751 Cys-Gly C01419 179.047394 0.704 gamma-L-Glutamyl-L-cysteine C00669 251.068329 0.782 gamma-L-Glutamyl-D-alanine C03738 219.097214 0.704 gamma-Glutamyl-gamma-aminobutyrate C15767 233.111893 0.711 10-Formyldihydrofolate C03204 472.154846 1.753 Ornithine C01602 133.096359 0.606 L-Citrulline C00327 176.102509 0.665 Putrescine C00134 89.106819 0.611 Spermidine C00315 146.164246 0.588 Spermine C00750 203.22168 0.585 Carnosine C00386 227.11235 0.605 N-Acetylornithine C00437 175.107269 0.708 Guanidinoacetate C00581 118.060463 0.661 trans-4-Hydroxy-L-proline C01157 132.064728 0.768 Taurine C00245 126.021202 0.668 L-Methionine S-oxide C02989 166.05188 0.784 Indole-3-acetate C00954 176.071976 1.757 Anthranilate C00108 138.054123 0.675 Picolinic acid C10164 124.039398 0.564 g-Oxalo-crotonate C03453 159.027084 0.713 N-Methylethanolamine phosphate C01210 156.041092 0.63 Sphingosine C00319 300.287811 2.021 Acetylcholine C01996 146.116653 0.69 Choline C00114 104.106445 0.65 L-Carnitine C00318 162.111389 0.659 acetyl-carnitine (acyl-C2) C02571 204.121674 0.707 propionyl-carnitine (acyl-C3) C03017 218.137238 0.725 butanoyl-l-carnitine (acyl-C4) C02862 232.152817 1.759 acyl-C4-OH HMDB13127 248.147629 0.711 acyl-C4-DC HMDB13133 262.127441 0.7 acyl-C5-OH ac107 262.163208 0.703 hexanoyl-L-carnitine (acyl-C6) HMDB00756 260.183777 1.821 O-dodecanoyl-carnitine (acyl-C12) HMDB02250 344.277405 1.964 O-dodecenoyl-carnitine (acyl-C12:1) HMDB13326 342.265991 2.771 O-tetradecanoyl-L-carnitine (acyl-C14) HMDB05066 372.309998 2.032 L-Palmitoylcarnitine (acyl-C16) C02990 400.339691 2.081 Hexadecenoyl-carnitine (acyl-C16:1) HMDB06317 398.324646 2.042 Octadecanoyl-L-carnitine (acyl-C18) HMDB00848 428.370758 2.136 O-octadecenoyl-L-carnitine (acyl-C18:1) HMDB06351 426.355438 2.09 acyl-C18:2 (Linoleoyl-CoA) HMDB01064 424.3396 2.049 acyl-C20:4 ac125 448.339447 2.042 Biliverdin C00500 583.245178 2.523 METABOLITES_END #END