{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002487","ANALYSIS_ID":"AN004061","VERSION":"1","CREATED_ON":"February 21, 2023, 9:03 am"},

"PROJECT":{"PROJECT_TITLE":"Simultaneous targeting of PD-1 and IL2Rβγ with radiation therapy to inhibit pancreatic cancer growth and metastasis","PROJECT_SUMMARY":"In pancreatic ductal adenocarcinoma (PDAC) patients, we show that response to radiation therapy (RT) is characterized by increased IL2Rβ and IL2Rγ and decreased ILR2α expression. The bispecific aPD1-IL2v is a PD-1-targeted IL-2 variant (IL2v) immunocytokine with engineered IL-2 cis-targeted to PD-1 and abolished IL2Rα binding, which enhances tumor-antigen specific T cell activation while reducing regulatory T cell (Treg) suppression. Using aPD1-IL2v in orthotopic PDAC KPC-driven tumor models, we show marked improvement in local and metastatic survival along with profound increase in tumor-infiltrating polyfunctional CD8+ T cell subsets with a transcriptionally and metabolically active phenotype, and preferential activation of antigen-specific CD8+ T cells. In combination with single dose RT, aPD1-IL2v treatment results in a robust, durable expansion of polyfunctional CD8+ T cells, T cell stemness, tumor-specific memory immune response, natural killer (NK) cell activation, and decreased Tregs. These data show that aPD1-IL2v leads to profound local and distant response in PDAC.","INSTITUTE":"University of Colorado Denver","LABORATORY":"Lab of Angelo D'Alessandro in collaboration with lab of Sana Karam","LAST_NAME":"Haines","FIRST_NAME":"Julie","ADDRESS":"12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA","EMAIL":"julie.haines@cuanschutz.edu","PHONE":"3037243339"},

"STUDY":{"STUDY_TITLE":"Simultaneous targeting of PD-1 and IL2Rβγ with radiation therapy to inhibit pancreatic cancer growth and metastasis - mouse spleen and lymph node T-cell metabolomics","STUDY_SUMMARY":"Mice were orthotopically implanted with PK5L1940 cells then radiation therapy (8 Gy) administered 7 days post-implantation. PD1-IL2v and aCD25 dosed once per week beginning day 7 post-implantation. Spleen and associated lymph nodes were collected at time of sacrifice and sorted for CD8+ T-cells. The obtained T-cells were profiled by mass spectrometry-based metabolomics.","INSTITUTE":"University of Colorado Denver","LAST_NAME":"Haines","FIRST_NAME":"Julie","ADDRESS":"12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA","EMAIL":"julie.haines@cuanschutz.edu","PHONE":"3037243339"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"MSL-1",
"Factors":{"factor":"Untrx"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-1-r4"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-2",
"Factors":{"factor":"Untrx"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-2-r5"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-3",
"Factors":{"factor":"Untrx"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-3-r6"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-4",
"Factors":{"factor":"RT"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-4-r13"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-5",
"Factors":{"factor":"RT"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-5-r9"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-6",
"Factors":{"factor":"RT"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-6-r7"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-7",
"Factors":{"factor":"IL2v"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-7-r12"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-8",
"Factors":{"factor":"IL2v"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-8-r15"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-9",
"Factors":{"factor":"IL2v"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-9-r14"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-10",
"Factors":{"factor":"RT+IL2v"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-10-r1"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-11",
"Factors":{"factor":"RT+IL2v"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-11-r8"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-12",
"Factors":{"factor":"RT+IL2v"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-12-r11"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-13",
"Factors":{"factor":"aCD25"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-13-r10"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-14",
"Factors":{"factor":"aCD25"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-14-r3"}
},
{
"Subject ID":"-",
"Sample ID":"MSL-15",
"Factors":{"factor":"aCD25"},
"Additional sample data":{"RAW_FILE_NAME":"AG-23-MSL-15-r2"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Spleens of C57BL/6 mice were homogenized to a single cell suspension by mashing the spleen through a 70 uM cell strainer, and the erythrocytes were lysed with ACK (ammonium-chloride-potassium) lysis buffer for 3 min at RT. CD8 T cells were sorted with a CD8-negative selection Stemcell isolation kit following manufacturer instructions. Cells were washed with PBS at 1200RPM, 4degC for 10 minutes and pellets were flash frozen.","SAMPLE_TYPE":"Spleen; T-cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Mice were orthotopically implanted with PK5L1940 cells. RT administered 7 days post-implantation. PD1-IL2v and aCD25 dosed once per week beginning day 7 post-implantation."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites from frozen T-cell pellets were extracted with cold 5:3:2 MeOH:acetonitrile:water at a concentration of 4 million cells/mL. Samples were vortexed 30 min at 4 degrees C then supernatants clarified by centrifugation (10 min, 10,000 g, 4 degrees C) and transferred to autosampler vials.","PROCESSING_STORAGE_CONDITIONS":"4℃","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Positive C18","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Phenomenex Kinetex C18 2.1 x 150 mm, 1.7 um","SOLVENT_A":"100% water 0.1% formic acid","SOLVENT_B":"100% acetonitrile 0.1% formic acid","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 95-5% B, 3-5 min hold at 5% B","FLOW_RATE":"450 uL/min","COLUMN_TEMPERATURE":"45","SAMPLE_INJECTION":"10 uL"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Orbitrap Exploris 480","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"We use a Thermo Orbitrap Exploris 120 (not available in the drop down box). Resolution 120,000, scan range 65-975 m/z, maximum injection time 100 ms, microscans 1, automatic gain control (AGC) detection duration 20 msec, source voltage 3.5 kV, capillary temperature 320 C, vaporizer temp 200 C, and sheath gas 50, auxiliary gas 10, and sweep gas 1 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database."},

"MS_METABOLITE_DATA":{
"Units":"peak area",

"Data":[{"Metabolite":"L-alanine","MSL-1":"6220456","MSL-2":"117104","MSL-3":"67206","MSL-4":"232560","MSL-5":"209320","MSL-6":"136396","MSL-7":"1903167","MSL-8":"203713","MSL-9":"758283","MSL-10":"372548","MSL-11":"161126","MSL-12":"568129","MSL-13":"72993","MSL-14":"307703","MSL-15":"41451"},{"Metabolite":"L-arginine","MSL-1":"2886038","MSL-2":"191098","MSL-3":"457760","MSL-4":"341649","MSL-5":"1918120","MSL-6":"624038","MSL-7":"2583023","MSL-8":"896678","MSL-9":"1808375","MSL-10":"1585220","MSL-11":"1158713","MSL-12":"2625003","MSL-13":"346805","MSL-14":"1450789","MSL-15":"289284"},{"Metabolite":"L-asparagine","MSL-1":"794468","MSL-2":"4887","MSL-3":"3822","MSL-4":"7360","MSL-5":"14597","MSL-6":"6429","MSL-7":"302934","MSL-8":"11431","MSL-9":"71365","MSL-10":"34281","MSL-11":"19935","MSL-12":"47180","MSL-13":"1106","MSL-14":"19273","MSL-15":"0"},{"Metabolite":"L-aspartate","MSL-1":"3201557","MSL-2":"75990","MSL-3":"105104","MSL-4":"55061","MSL-5":"274961","MSL-6":"46707","MSL-7":"1857177","MSL-8":"295597","MSL-9":"774993","MSL-10":"476964","MSL-11":"202489","MSL-12":"502550","MSL-13":"218718","MSL-14":"282114","MSL-15":"96994"},{"Metabolite":"L-glutamate","MSL-1":"7578056","MSL-2":"214302","MSL-3":"192026","MSL-4":"325565","MSL-5":"608511","MSL-6":"169620","MSL-7":"3559566","MSL-8":"451774","MSL-9":"1501267","MSL-10":"778142","MSL-11":"366914","MSL-12":"835883","MSL-13":"166203","MSL-14":"526636","MSL-15":"229258"},{"Metabolite":"L-glutamine","MSL-1":"1612133","MSL-2":"272552","MSL-3":"19963","MSL-4":"229407","MSL-5":"45368","MSL-6":"84006","MSL-7":"471571","MSL-8":"49128","MSL-9":"136689","MSL-10":"68894","MSL-11":"29231","MSL-12":"83019","MSL-13":"8462","MSL-14":"116132","MSL-15":"11504"},{"Metabolite":"glycine","MSL-1":"1239623","MSL-2":"10735","MSL-3":"23514","MSL-4":"20886","MSL-5":"65159","MSL-6":"21283","MSL-7":"718253","MSL-8":"90323","MSL-9":"236076","MSL-10":"154441","MSL-11":"69852","MSL-12":"172582","MSL-13":"43856","MSL-14":"73421","MSL-15":"13812"},{"Metabolite":"L-histidine","MSL-1":"710123","MSL-2":"49858","MSL-3":"20481","MSL-4":"65561","MSL-5":"42014","MSL-6":"43961","MSL-7":"165468","MSL-8":"11304","MSL-9":"58459","MSL-10":"24712","MSL-11":"17074","MSL-12":"82709","MSL-13":"11444","MSL-14":"25335","MSL-15":"9395"},{"Metabolite":"L-leucine/isoleucine","MSL-1":"10456415","MSL-2":"325719","MSL-3":"183455","MSL-4":"769155","MSL-5":"1159944","MSL-6":"394607","MSL-7":"3938987","MSL-8":"556164","MSL-9":"1665555","MSL-10":"783760","MSL-11":"498344","MSL-12":"1547486","MSL-13":"136166","MSL-14":"902696","MSL-15":"217865"},{"Metabolite":"L-lysine","MSL-1":"2702733","MSL-2":"35898","MSL-3":"88980","MSL-4":"73284","MSL-5":"477946","MSL-6":"114755","MSL-7":"690459","MSL-8":"120055","MSL-9":"246987","MSL-10":"218934","MSL-11":"227769","MSL-12":"382202","MSL-13":"65169","MSL-14":"222843","MSL-15":"116629"},{"Metabolite":"L-methionine","MSL-1":"6181472","MSL-2":"34928","MSL-3":"53995","MSL-4":"80290","MSL-5":"420220","MSL-6":"94438","MSL-7":"1910100","MSL-8":"272219","MSL-9":"998755","MSL-10":"412832","MSL-11":"200108","MSL-12":"720949","MSL-13":"70971","MSL-14":"415375","MSL-15":"64399"},{"Metabolite":"L-phenylalanine","MSL-1":"2734763","MSL-2":"65302","MSL-3":"123115","MSL-4":"106958","MSL-5":"825918","MSL-6":"126174","MSL-7":"820303","MSL-8":"179280","MSL-9":"421134","MSL-10":"299674","MSL-11":"287310","MSL-12":"506307","MSL-13":"57061","MSL-14":"277735","MSL-15":"211003"},{"Metabolite":"L-serine","MSL-1":"1555051","MSL-2":"31735","MSL-3":"10217","MSL-4":"50684","MSL-5":"33883","MSL-6":"10585","MSL-7":"662047","MSL-8":"16396","MSL-9":"154625","MSL-10":"71373","MSL-11":"27721","MSL-12":"103289","MSL-13":"14675","MSL-14":"38132","MSL-15":"4371"},{"Metabolite":"L-threonine","MSL-1":"2453774","MSL-2":"50177","MSL-3":"23451","MSL-4":"77141","MSL-5":"71923","MSL-6":"49482","MSL-7":"1057199","MSL-8":"86094","MSL-9":"282792","MSL-10":"131270","MSL-11":"56025","MSL-12":"251214","MSL-13":"17327","MSL-14":"105852","MSL-15":"6806"},{"Metabolite":"L-tryptophan","MSL-1":"5338840","MSL-2":"209066","MSL-3":"589131","MSL-4":"304742","MSL-5":"1577107","MSL-6":"642589","MSL-7":"1146148","MSL-8":"448310","MSL-9":"754948","MSL-10":"1034001","MSL-11":"912880","MSL-12":"1949160","MSL-13":"210137","MSL-14":"597696","MSL-15":"555969"},{"Metabolite":"L-tyrosine","MSL-1":"6320108","MSL-2":"154481","MSL-3":"100482","MSL-4":"326924","MSL-5":"461403","MSL-6":"171455","MSL-7":"1934298","MSL-8":"424388","MSL-9":"1079202","MSL-10":"786238","MSL-11":"320510","MSL-12":"1122202","MSL-13":"98129","MSL-14":"439945","MSL-15":"152537"},{"Metabolite":"L-valine","MSL-1":"13710311","MSL-2":"4825861","MSL-3":"4195560","MSL-4":"4782457","MSL-5":"9913964","MSL-6":"5772354","MSL-7":"7666969","MSL-8":"3873959","MSL-9":"7077381","MSL-10":"4421966","MSL-11":"2255006","MSL-12":"5793172","MSL-13":"2057224","MSL-14":"3259788","MSL-15":"1341740"},{"Metabolite":"AMP","MSL-1":"10700347","MSL-2":"99837","MSL-3":"2739896","MSL-4":"97465","MSL-5":"7348932"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ID":"C01835","parent":"505.177979","medRt":"2.182"},{"Metabolite":"Glutathione","KEGG ID":"C00051","parent":"308.089325","medRt":"0.699"},{"Metabolite":"Glutathione disulfide","KEGG ID":"C00127","parent":"613.156677","medRt":"0.712"},{"Metabolite":"5-Oxoproline","KEGG ID":"C01879","parent":"130.049088","medRt":"0.751"},{"Metabolite":"Cys-Gly","KEGG ID":"C01419","parent":"179.047394","medRt":"0.704"},{"Metabolite":"gamma-L-Glutamyl-L-cysteine","KEGG ID":"C00669","parent":"251.068329","medRt":"0.782"},{"Metabolite":"gamma-L-Glutamyl-D-alanine","KEGG ID":"C03738","parent":"219.097214","medRt":"0.704"},{"Metabolite":"gamma-Glutamyl-gamma-aminobutyrate","KEGG ID":"C15767","parent":"233.111893","medRt":"0.711"},{"Metabolite":"10-Formyldihydrofolate","KEGG ID":"C03204","parent":"472.154846","medRt":"1.753"},{"Metabolite":"Ornithine","KEGG ID":"C01602","parent":"133.096359","medRt":"0.606"},{"Metabolite":"L-Citrulline","KEGG ID":"C00327","parent":"176.102509","medRt":"0.665"},{"Metabolite":"Putrescine","KEGG ID":"C00134","parent":"89.106819","medRt":"0.611"},{"Metabolite":"Spermidine","KEGG ID":"C00315","parent":"146.164246","medRt":"0.588"},{"Metabolite":"Spermine","KEGG ID":"C00750","parent":"203.22168","medRt":"0.585"},{"Metabolite":"Carnosine","KEGG ID":"C00386","parent":"227.11235","medRt":"0.605"},{"Metabolite":"N-Acetylornithine","KEGG ID":"C00437","parent":"175.107269","medRt":"0.708"},{"Metabolite":"Guanidinoacetate","KEGG ID":"C00581","parent":"118.060463","medRt":"0.661"},{"Metabolite":"trans-4-Hydroxy-L-proline","KEGG ID":"C01157","parent":"132.064728","medRt":"0.768"},{"Metabolite":"Taurine","KEGG ID":"C00245","parent":"126.021202","medRt":"0.668"},{"Metabolite":"L-Methionine S-oxide","KEGG ID":"C02989","parent":"166.05188","medRt":"0.784"},{"Metabolite":"Indole-3-acetate","KEGG ID":"C00954","parent":"176.071976","medRt":"1.757"},{"Metabolite":"Anthranilate","KEGG ID":"C00108","parent":"138.054123","medRt":"0.675"},{"Metabolite":"Picolinic acid","KEGG ID":"C10164","parent":"124.039398","medRt":"0.564"},{"Metabolite":"g-Oxalo-crotonate","KEGG ID":"C03453","parent":"159.027084","medRt":"0.713"},{"Metabolite":"N-Methylethanolamine phosphate","KEGG ID":"C01210","parent":"156.041092","medRt":"0.63"},{"Metabolite":"Sphingosine","KEGG ID":"C00319","parent":"300.287811","medRt":"2.021"},{"Metabolite":"Acetylcholine","KEGG ID":"C01996","parent":"146.116653","medRt":"0.69"},{"Metabolite":"Choline","KEGG ID":"C00114","parent":"104.106445","medRt":"0.65"},{"Metabolite":"L-Carnitine","KEGG ID":"C00318","parent":"162.111389","medRt":"0.659"},{"Metabolite":"acetyl-carnitine (acyl-C2)","KEGG ID":"C02571","parent":"204.121674","medRt":"0.707"},{"Metabolite":"propionyl-carnitine (acyl-C3)","KEGG ID":"C03017","parent":"218.137238","medRt":"0.725"},{"Metabolite":"butanoyl-l-carnitine (acyl-C4)","KEGG ID":"C02862","parent":"232.152817","medRt":"1.759"},{"Metabolite":"acyl-C4-OH","KEGG ID":"HMDB13127","parent":"248.147629","medRt":"0.711"},{"Metabolite":"acyl-C4-DC","KEGG ID":"HMDB13133","parent":"262.127441","medRt":"0.7"},{"Metabolite":"acyl-C5-OH","KEGG ID":"ac107","parent":"262.163208","medRt":"0.703"},{"Metabolite":"hexanoyl-L-carnitine (acyl-C6)","KEGG ID":"HMDB00756","parent":"260.183777","medRt":"1.821"},{"Metabolite":"O-dodecanoyl-carnitine (acyl-C12)","KEGG ID":"HMDB02250","parent":"344.277405","medRt":"1.964"},{"Metabolite":"O-dodecenoyl-carnitine (acyl-C12:1)","KEGG ID":"HMDB13326","parent":"342.265991","medRt":"2.771"},{"Metabolite":"O-tetradecanoyl-L-carnitine (acyl-C14)","KEGG ID":"HMDB05066","parent":"372.309998","medRt":"2.032"},{"Metabolite":"L-Palmitoylcarnitine (acyl-C16)","KEGG ID":"C02990","parent":"400.339691","medRt":"2.081"},{"Metabolite":"Hexadecenoyl-carnitine (acyl-C16:1)","KEGG ID":"HMDB06317","parent":"398.324646","medRt":"2.042"},{"Metabolite":"Octadecanoyl-L-carnitine (acyl-C18)","KEGG ID":"HMDB00848","parent":"428.370758","medRt":"2.136"},{"Metabolite":"O-octadecenoyl-L-carnitine (acyl-C18:1)","KEGG ID":"HMDB06351","parent":"426.355438","medRt":"2.09"},{"Metabolite":"acyl-C18:2 (Linoleoyl-CoA)","KEGG ID":"HMDB01064","parent":"424.3396","medRt":"2.049"},{"Metabolite":"acyl-C20:4","KEGG ID":"ac125","parent":"448.339447","medRt":"2.042"},{"Metabolite":"Biliverdin","KEGG ID":"C00500","parent":"583.245178","medRt":"2.523"}]
}

}