#METABOLOMICS WORKBENCH juliehaines_20230509_073244 DATATRACK_ID:4015 STUDY_ID:ST002712 ANALYSIS_ID:AN004396 PROJECT_ID:PR001681 VERSION 1 CREATED_ON May 25, 2023, 12:37 pm #PROJECT PR:PROJECT_TITLE Ranolazine induced metabolic rewiring improves melanoma responses to targeted PR:PROJECT_TITLE therapy and immunotherapy PR:PROJECT_SUMMARY Metabolic rewiring affects resistance of melanoma to targeted- and PR:PROJECT_SUMMARY immuno-therapy. We have found that increased fatty acid oxidation (FAO) during PR:PROJECT_SUMMARY late stages of BRAF inhibitor (BRAFi) treatment enables the establishment of PR:PROJECT_SUMMARY acquired resistance. Targeting FAO with ranolazine in vivo once acquired PR:PROJECT_SUMMARY BRAFi-resistance emerges delays tumour recurrence. Single cell RNAseq analysis PR:PROJECT_SUMMARY revealed that ranolazine diminishes the transcriptional NGFRhigh neural crest PR:PROJECT_SUMMARY stem cell subpopulation, which is refractory against BRAFi and immunotherapy. PR:PROJECT_SUMMARY Moreover, by rewiring the methionine salvage pathway, ranolazine enhanced PR:PROJECT_SUMMARY melanoma immunogenicity through increased antigen presentation and interferon PR:PROJECT_SUMMARY signalling. Combination of ranolazine with anti-PD-L1 antibodies strongly PR:PROJECT_SUMMARY improved survival in mice, where it increased lymphocyte infiltration and PR:PROJECT_SUMMARY enhanced anti-tumour responses. Altogether, we show that ranolazine increases PR:PROJECT_SUMMARY the efficacy of targeted melanoma therapy through fatty acid and methionine PR:PROJECT_SUMMARY salvage metabolic rewiring. Importantly, our study suggests that ranolazine PR:PROJECT_SUMMARY could sensitize BRAFi-resistant tumours to immunotherapy, by modulating melanoma PR:PROJECT_SUMMARY cell recognition and immune infiltration. Ranolazine is an FDA and EMA-approved PR:PROJECT_SUMMARY anti-anginal drug with very mild side effects, and our preclinical data PR:PROJECT_SUMMARY encourage its use as a therapeutic option to improve the two main therapeutic PR:PROJECT_SUMMARY strategies currently used to treat metastatic melanoma. PR:INSTITUTE University of Colorado Denver PR:LABORATORY Lab of Angelo D'Alessandro in collaboration with lab of Imanol Arozarena 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 Ranolazine induced metabolic rewiring improves melanoma responses to targeted ST:STUDY_TITLE therapy and immunotherapy - metabolomics ST:STUDY_SUMMARY Metabolomics analysis was performed on A375 melanoma cells resistant to BRAF ST:STUDY_SUMMARY inhibitor vemurafenib (VR) and cells resistant to VR and treated with fatty acid ST:STUDY_SUMMARY oxidation inhibitor ranolazine. 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 Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:GENDER Female SU:CELL_BIOSOURCE_OR_SUPPLIER ATCC SU:CELL_STRAIN_DETAILS A375 #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 - A375P 5 Treatment:VEHICLE RAW_FILE_NAME=AG-M-1 SUBJECT_SAMPLE_FACTORS - A375P 6 Treatment:VEHICLE RAW_FILE_NAME=AG-M-2 SUBJECT_SAMPLE_FACTORS - A375P 7 Treatment:VEHICLE RAW_FILE_NAME=AG-M-3 SUBJECT_SAMPLE_FACTORS - A375P 8 Treatment:VEHICLE RAW_FILE_NAME=AG-M-4 SUBJECT_SAMPLE_FACTORS - A375 VR 5 Treatment:VEMURA RAW_FILE_NAME=AG-M-5 SUBJECT_SAMPLE_FACTORS - A375 VR 6 Treatment:VEMURA RAW_FILE_NAME=AG-M-6 SUBJECT_SAMPLE_FACTORS - A375 VR 7 Treatment:VEMURA RAW_FILE_NAME=AG-M-7 SUBJECT_SAMPLE_FACTORS - A375 VR 8 Treatment:VEMURA RAW_FILE_NAME=AG-M-8 SUBJECT_SAMPLE_FACTORS - A375 VR-Rano 5 Treatment:VEMURA+RANO RAW_FILE_NAME=AG-M-9 SUBJECT_SAMPLE_FACTORS - A375 VR-Rano 6 Treatment:VEMURA+RANO RAW_FILE_NAME=AG-M-10 SUBJECT_SAMPLE_FACTORS - A375 VR-Rano 7 Treatment:VEMURA+RANO RAW_FILE_NAME=AG-M-11 SUBJECT_SAMPLE_FACTORS - A375 VR-Rano 8 Treatment:VEMURA+RANO RAW_FILE_NAME=AG-M-12 #COLLECTION CO:COLLECTION_SUMMARY All cell lines had been authenticated in 2021. Cells were expanded to generate CO:COLLECTION_SUMMARY enough vials from a single batch before the start of the study. Cell lines were CO:COLLECTION_SUMMARY cultured in Dulbecco’s Eagle’s Medium (DMEM) (cat#61965026, Gibco) CO:COLLECTION_SUMMARY supplemented with 10% fetal bovine serum (cat#10500064, Gibco) plus 1% CO:COLLECTION_SUMMARY penicillin/streptomycin (cat#15140122, Gibco). Cells were grown at 37°C in a 5% CO:COLLECTION_SUMMARY CO2 environment. CO:SAMPLE_TYPE Melanoma cells #TREATMENT TR:TREATMENT_SUMMARY Melanoma cells seeded in 6-well plates were treated for 7 days with a high dose TR:TREATMENT_SUMMARY (5 or 10μM as indicated) of vemurafenib before switching to a lower TR:TREATMENT_SUMMARY concentration of the drug (0,5 or 1μM). Fresh medium and vemurafenib was added TR:TREATMENT_SUMMARY once weekly for further 3-4 weeks until arising colonies grew to confluence. TR:TREATMENT_SUMMARY Fatty Acid oxidation inhibitors ranolazine, etomoxir or thiroridazine were added TR:TREATMENT_SUMMARY once a week. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Metabolites from frozen cell pellets were extracted with cold 5:3:2 SP:SAMPLEPREP_SUMMARY MeOH:acetonitrile:water at a concentration of 2 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 (150 x 2.1mm,1.7um) 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 A375P 5 A375P 6 A375P 7 A375P 8 A375 VR 5 A375 VR 6 A375 VR 7 A375 VR 8 A375 VR-Rano 5 A375 VR-Rano 6 A375 VR-Rano 7 A375 VR-Rano 8 Factors Treatment:VEHICLE Treatment:VEHICLE Treatment:VEHICLE Treatment:VEHICLE Treatment:VEMURA Treatment:VEMURA Treatment:VEMURA Treatment:VEMURA Treatment:VEMURA+RANO Treatment:VEMURA+RANO Treatment:VEMURA+RANO Treatment:VEMURA+RANO L-alanine 1873299 1839249 960536 1449300 1017454 761078 582263 750160 605128 489356 522599 689910 L-arginine 790670 875694 790815 841990 1405993 1232484 1438302 1696229 1057014 1522084 813558 1535090 L-asparagine 15533 14431 19767 28455 193050 215190 241579 305134 103194 80326 74205 127645 L-aspartate 172475 192749 185383 193803 410353 369211 419312 480910 231425 336655 226576 380082 L-cysteine 13152 37748 25093 25438 20824 8896 14525 12593 8777 20522 6401 17866 L-glutamate 7923250 7960536 6027780 8106199 4435238 3718165 3283682 4156250 2641219 2856216 2281330 3149223 L-glutamine 935982 944938 647313 914996 682121 683041 510702 554099 207697 180960 190611 274676 L-leucine/isoleucine 28326898 27728438 16190471 22520454 10938471 7327908 6561877 8064346 4868628 6354737 4895567 7719636 L-lysine 582956 463776 360100 465812 806131 600286 642685 718441 472182 536090 373525 542847 L-methionine 936779 879792 262683 698037 117522 26994 26023 54914 47968 96970 60804 150504 L-phenylalanine 8641149 7749052 4062540 6054651 2773605 2120235 1737321 2202108 2492144 2135230 2837171 2788470 L-proline 6426087 5863670 7431394 8379210 5952690 4920444 4260070 5237115 5353635 4661896 5457078 5704532 L-threonine 1559574 1501894 815657 1305492 584356 449412 331694 451658 462217 485371 411855 556418 L-tryptophan 34179836 29341934 15643304 22682026 9337091 7388415 5831083 7805330 9611108 7783963 9922408 10433795 L-tyrosine 7439467 6601476 3832023 6603968 3172631 2331310 1922002 2386512 1962329 1916696 1941655 2592297 L-valine 16616528 14271747 8159048 12927261 6511198 5184616 4489852 5552623 4698647 4190017 4530799 5648100 AMP 500204 323832 381710 449967 408555 242301 322334 348950 231466 177191 197621 212193 dAMP 149980 169246 152720 212354 56918 37141 10700 57985 67786 50832 68370 75803 Adenosine 179504 240410 97121 94972 3207024 3282300 2897682 3516796 4420556 5011320 4070454 7361396 Adenine 35978 38498 13614 46814 2599445 1237895 2313344 1491431 4923827 7269782 4918908 8213243 GMP 62749 42999 40341 36084 80037 90779 162032 106224 36080 32585 27990 40581 Guanine 3486 2462 3371 0 177472 155628 282785 229775 309869 481151 349861 506801 CMP 117832 122329 104992 103694 67178 30022 48836 40961 9607 24242 15622 34181 Cytidine 12962 0 5826 4531 801355 817768 742715 960921 63980 93245 75397 61620 Cytosine 22512 10588 7285 9143 36307 35106 37254 50098 44303 39610 32203 48347 Allantoate 3986 0 7244 12765 18257 13934 8938 13496 7470 7729 2541 10249 Pyridoxal 69509 67149 82409 79194 106512 90364 93823 100155 43983 59773 38220 41981 Pyridoxamine 5'-phosphate 52349 64231 31502 27450 22138 7749 15705 18496 23525 15650 21112 18641 Nicotinamide 365491 308368 269760 313971 445085 461019 401449 401892 225784 303336 248515 354877 NAD+ 471791 544049 508421 614358 519236 340553 266550 386206 379532 393236 291626 339304 D-Rhamnose 16680840 25219018 27769254 17497266 15703388 26357600 18906758 21236528 15700227 19101534 18837576 24079434 D-Glucono-1-5-lactone 6-phosphate 17620 15572 33091 55542 1247083 1073641 677757 996893 33476 62130 21118 48552 Glutathione disulfide 88578 62671 101804 61881 49051 44382 40257 65549 91660 128237 130900 93027 Cys-Gly 259124 242762 246977 322035 77250 60091 48831 62636 59281 78414 91058 95726 gamma-L-Glutamyl-L-cysteine 74608 51273 47120 39402 18489 5472 16104 6735 22506 41136 34064 47416 Folate 2606 4278 0 0 47069 50374 41640 51406 11796 9441 13946 10043 L-Citrulline 7990 9388 10526 17539 51024 77396 66810 60151 18540 11225 6305 10800 Cadaverine 58461 40945 15485 53362 5986 0 2195 6915 2014 0 0 0 Putrescine 173887 151309 158047 138998 177630 164317 144173 136013 210107 193904 225710 215898 Spermidine 1089757 770008 578086 659091 489336 705900 429592 479359 2017155 1022277 2853389 1352301 Spermine 1222497 1123532 1193104 2063535 1497297 2063300 753993 841021 1617900 2551021 2487966 1438571 Homocarnosine 80013 71681 61077 62593 85490 94179 73755 90255 78966 71594 71530 69237 Creatine 30444446 28342112 32876776 34654436 11466475 9274064 7658478 10010311 16259255 14251531 15225801 16553985 Creatinine 135032 130569 116624 137325 61067 54019 31200 35580 44466 30752 57571 47419 N-Acetylornithine 82926 105883 53546 87262 75874 45122 56596 70397 87897 81474 73225 86150 Taurine 102445 98146 176424 209882 71792 72123 45436 57085 40916 36758 42215 60605 L-Methionine S-oxide 1353473 1294312 841788 1218954 651018 438240 364515 484754 440285 411780 383958 561842 3-Methyleneoxindole 282525 226850 111795 179657 77147 53130 47889 47175 68829 66531 84459 88847 Indole-3-acetaldehyde 40625 40664 21744 24317 14110 7082 6241 11790 9376 8437 17407 21402 Indole-3-acetate 151368 161946 160373 155838 185336 192680 149006 243072 30407 26977 40175 55650 Indolepyruvate 172686 124115 105182 131440 44167 47360 35073 26778 39737 32013 38895 35567 g-Oxalo-crotonate 4690 2166 2028 0 1446580 1571199 1540488 1811832 178236 190960 128153 308675 2-Aminomuconate 214579 199964 222997 313711 38300 27043 21227 33144 40533 64678 28482 55602 Sphingosine 8404317 7650043 3291069 5672290 2533072 1797035 2203390 2034944 2778907 3057142 2276300 2942783 Acetylcholine 540257 503567 805064 903379 265767 229136 175666 224340 106879 96659 104976 137168 Choline 29814186 23574576 20667490 19311790 32413914 24633776 22201254 22837704 20538598 21361154 16491917 24445570 L-Carnitine 5483687 5209009 8477085 10655361 3169660 2911833 2403490 2373763 894349 909492 1010134 1047069 acetyl-carnitine (acyl-C2) 10741133 8820753 10800963 11225421 1776042 2064592 1646783 1901633 827221 769515 966873 879709 propionyl-carnitine (acyl-C3) 1492554 1367265 3776090 3416667 553828 504219 421475 548174 155358 175380 186791 234551 butanoyl-l-carnitine (acyl-C4) 970528 889383 655848 995943 42670 36387 27638 34092 97813 57969 97795 80223 O-tetradecanoyl-L-carnitine (acyl-C14) 1319845 1269626 901796 1087468 65452 68192 37119 59716 60006 59937 89692 91904 L-Palmitoylcarnitine (acyl-C16) 368964 286320 258852 295363 31388 28642 25232 25336 48609 32285 34529 55789 Hexadecenoyl-carnitine (acyl-C16:1) 254481 254905 221121 207753 66944 94661 49141 58906 44565 33030 34445 56621 O-octadecenoyl-L-carnitine (acyl-C18:1) 83157 59955 71968 71980 19707 19239 13046 17220 18525 13112 19981 19177 S-Adenosyl-L-methionine 95320 98700 81863 149918 58293 31908 51495 76496 7897 28269 7902 30053 5-Methylthioadenosine 1154343 976901 561470 745014 338005 300296 299699 346269 446200 345353 398574 621518 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name KEGG ID m/z r.t. (min) L-alanine C00041 90.0551 0.6670 L-arginine C00062 175.1189 0.6330 L-asparagine C00152 133.0602 0.6590 L-aspartate C00049 134.0449 0.6870 L-cysteine C00097 122.0272 0.7040 L-glutamate C00025 148.0605 0.6960 L-glutamine C00064 147.0764 0.6590 L-leucine/isoleucine C00123 132.1020 0.7610 L-lysine C00047 147.1128 0.6030 L-methionine C00073 150.0583 0.7120 L-phenylalanine C00079 166.0856 1.4020 L-proline C00148 116.0707 0.6870 L-threonine C00188 120.0657 0.6640 L-tryptophan C00078 205.0972 1.7740 L-tyrosine C00082 182.0810 0.7230 L-valine C00183 118.0864 0.7100 AMP C00020 348.070312 0.833 dAMP C00360 332.077576 0.693 Adenosine C00212 268.104034 0.709 Adenine C00147 136.061813 0.758 GMP C00144 364.065338 0.695 Guanine C00242 152.056732 0.744 CMP C00055 324.059174 0.68 Cytidine C00475 244.092896 1.883 Cytosine C00380 112.050751 0.689 Allantoate C00499 177.061554 0.625 Pyridoxal C00250 168.065201 0.681 Pyridoxamine 5'-phosphate C00647 249.061249 1.776 Nicotinamide C00153 123.055412 0.752 NAD+ C00003 664.116943 0.684 D-Rhamnose C01684 165.076004 2.044 D-Glucono-1-5-lactone 6-phosphate C01236 259.021362 0.755 Glutathione disulfide C00127 613.15979 0.695 Cys-Gly C01419 179.048584 0.703 gamma-L-Glutamyl-L-cysteine C00669 251.069794 0.696 Folate C00504 442.147339 1.769 L-Citrulline C00327 176.102997 0.668 Cadaverine C01672 103.123146 0.626 Putrescine C00134 89.107437 0.645 Spermidine C00315 146.165207 0.662 Spermine C00750 203.223053 0.628 Homocarnosine C00884 241.131165 2.574 Creatine C00300 132.076874 0.677 Creatinine C00791 114.066322 0.674 N-Acetylornithine C00437 175.107681 0.683 Taurine C00245 126.022018 0.713 L-Methionine S-oxide C02989 166.053177 0.698 3-Methyleneoxindole C02796 146.060059 1.782 Indole-3-acetaldehyde C00637 160.075684 1.781 Indole-3-acetate C00954 176.070587 1.973 Indolepyruvate C00331 204.063126 0.693 g-Oxalo-crotonate C03453 159.028061 0.756 2-Aminomuconate C02220 158.044815 0.744 Sphingosine C00319 300.289673 2.103 Acetylcholine C01996 146.117615 0.692 Choline C00114 104.107155 0.665 L-Carnitine C00318 162.112503 0.667 acetyl-carnitine (acyl-C2) C02571 204.123032 0.702 propionyl-carnitine (acyl-C3) C03017 218.138687 0.74 butanoyl-l-carnitine (acyl-C4) C02862 232.154312 1.734 O-tetradecanoyl-L-carnitine (acyl-C14) HMDB05066 372.311005 2.141 L-Palmitoylcarnitine (acyl-C16) C02990 400.342133 2.469 Hexadecenoyl-carnitine (acyl-C16:1) HMDB06317 398.327179 2.184 O-octadecenoyl-L-carnitine (acyl-C18:1) HMDB06351 426.358093 2.546 S-Adenosyl-L-methionine C00019 399.144409 0.667 5-Methylthioadenosine C00170 298.096802 1.762 METABOLITES_END #END