#METABOLOMICS WORKBENCH cendalfr_20240411_082827 DATATRACK_ID:4772 STUDY_ID:ST003170 ANALYSIS_ID:AN005202 PROJECT_ID:PR001970
VERSION             	1
CREATED_ON             	April 11, 2024, 8:36 am
#PROJECT
PR:PROJECT_TITLE                 	Releasing the mitochondrial respiration brake MCJ/DnaJC15 enhances CD8 CAR-T
PR:PROJECT_TITLE                 	cell therapy efficacy
PR:PROJECT_SUMMARY               	Metabolism of chimeric antigen receptor (CAR) T cells is emerging as an
PR:PROJECT_SUMMARY               	important area to improve CAR-T cell therapy in cancer treatment. Mitochondrial
PR:PROJECT_SUMMARY               	respiration is essential for survival and function of CAR-T cells, but
PR:PROJECT_SUMMARY               	developing strategies to specifically enhance mitochondrial respiration has been
PR:PROJECT_SUMMARY               	challenging. Here we identify MCJ/DnaJC15, an endogenous negative regulator of
PR:PROJECT_SUMMARY               	mitochondrial Complex I, as a metabolic target to enhance mitochondrial
PR:PROJECT_SUMMARY               	respiration in CD8 CAR-T cells. Loss of MCJ in CD8 CAR-T cells increases their
PR:PROJECT_SUMMARY               	in vitro and in vivo efficacy against mouse B cell leukemias. MCJ deficiency in
PR:PROJECT_SUMMARY               	TCR- specific CD8 cells also increases their efficacy against solid tumors in
PR:PROJECT_SUMMARY               	vivo. Furthermore, we reveal that human CD8 cells express MCJ and that silencing
PR:PROJECT_SUMMARY               	MCJ expression increases mitochondrial metabolism and anti-tumor activity of
PR:PROJECT_SUMMARY               	human CAR-T cells. Thus, targeting MCJ to enhance mitochondrial metabolism is a
PR:PROJECT_SUMMARY               	promising therapeutic strategy to improve the efficacy of adoptive T cell
PR:PROJECT_SUMMARY               	therapies.
PR:INSTITUTE                     	University of Colorado School of Medicine
PR:LABORATORY                    	Laboratory of Angelo D'Alessandro in collaboration with Mercedes Rincon
PR:LAST_NAME                     	Cendali
PR:FIRST_NAME                    	Francesca
PR:ADDRESS                       	13199 East Montview Boulevard, Aurora, CO, 80045, USA
PR:EMAIL                         	francesca.cendali@cuanschutz.edu
PR:PHONE                         	3037246131
#STUDY
ST:STUDY_TITLE                   	Releasing the mitochondrial respiration brake MCJ/DnaJC15 enhances CD8 CAR-T
ST:STUDY_TITLE                   	cell therapy efficacy
ST:STUDY_SUMMARY                 	Metabolism of chimeric antigen receptor (CAR) T cells is emerging as an
ST:STUDY_SUMMARY                 	important area to improve CAR-T cell therapy in cancer treatment. Mitochondrial
ST:STUDY_SUMMARY                 	respiration is essential for survival and function of CAR-T cells, but
ST:STUDY_SUMMARY                 	developing strategies to specifically enhance mitochondrial respiration has been
ST:STUDY_SUMMARY                 	challenging. Here we identify MCJ/DnaJC15, an endogenous negative regulator of
ST:STUDY_SUMMARY                 	mitochondrial Complex I, as a metabolic target to enhance mitochondrial
ST:STUDY_SUMMARY                 	respiration in CD8 CAR-T cells. Loss of MCJ in CD8 CAR-T cells increases their
ST:STUDY_SUMMARY                 	in vitro and in vivo efficacy against mouse B cell leukemias. MCJ deficiency in
ST:STUDY_SUMMARY                 	TCR- specific CD8 cells also increases their efficacy against solid tumors in
ST:STUDY_SUMMARY                 	vivo. Furthermore, we reveal that human CD8 cells express MCJ and that silencing
ST:STUDY_SUMMARY                 	MCJ expression increases mitochondrial metabolism and anti-tumor activity of
ST:STUDY_SUMMARY                 	human CAR-T cells. Thus, targeting MCJ to enhance mitochondrial metabolism is a
ST:STUDY_SUMMARY                 	promising therapeutic strategy to improve the efficacy of adoptive T cell
ST:STUDY_SUMMARY                 	therapies.
ST:INSTITUTE                     	University of Colorado School of Medicine
ST:LABORATORY                    	Laboratory of Angelo D'Alessandro in collaboration with Mercedes Rincon
ST:LAST_NAME                     	Cendali
ST:FIRST_NAME                    	Francesca
ST:ADDRESS                       	13199 East Montview Boulevard, Aurora, CO, 80045, USA
ST:EMAIL                         	francesca.cendali@cuanschutz.edu
ST:PHONE                         	3037246131
#SUBJECT
SU:SUBJECT_TYPE                  	Cultured cells
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           	-	A	Factor:WT CART med | Sample source:Cells	RAW_FILE_NAME(Raw File Name)=1
SUBJECT_SAMPLE_FACTORS           	-	B	Factor:WT CART med | Sample source:Cells	RAW_FILE_NAME(Raw File Name)=2
SUBJECT_SAMPLE_FACTORS           	-	C	Factor:WT CART med | Sample source:Cells	RAW_FILE_NAME(Raw File Name)=3
SUBJECT_SAMPLE_FACTORS           	-	D	Factor:MCJ KO CART med | Sample source:Cells	RAW_FILE_NAME(Raw File Name)=4
SUBJECT_SAMPLE_FACTORS           	-	E	Factor:MCJ KO CART med | Sample source:Cells	RAW_FILE_NAME(Raw File Name)=5
SUBJECT_SAMPLE_FACTORS           	-	F	Factor:MCJ KO CART med | Sample source:Cells	RAW_FILE_NAME(Raw File Name)=6
#COLLECTION
CO:COLLECTION_SUMMARY            	Murine CD8 cells were isolated from lymph nodes and spleen using negative
CO:COLLECTION_SUMMARY            	selection with CD8+ T cell isolation kit (for generation of CAR-T cells)
CO:COLLECTION_SUMMARY            	(Miltenyi, order# 130-104-075) or positive selection (for OT-I CD8 cells) with
CO:COLLECTION_SUMMARY            	CD8 (Ly-2) Microbeads (Miltenyi, order# 130-117-044). Mouse CD8 cells were
CO:COLLECTION_SUMMARY            	activated with plate-bound anti-CD3 (5 g/ml) and soluble anti-CD28 mAbs (1
CO:COLLECTION_SUMMARY            	g/ml) for 48h for WT and cMCJ KO CD8 studies and OT-I CD8 cells studies.
CO:SAMPLE_TYPE                   	T-cells
#TREATMENT
TR:TREATMENT_SUMMARY             	Metabolomics differences in this experiment are observed at baseline
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	CAR-T cells were isolated as described above either from in vitro culture or
SP:SAMPLEPREP_SUMMARY            	from bone marrow harvested in an in vivo study. The cells were washed in PBS and
SP:SAMPLEPREP_SUMMARY            	frozen at -80C until the assay is ready to run. Metabolites from cells were
SP:SAMPLEPREP_SUMMARY            	extracted at 2x106 cells/ml at 4°C (30 min) in the presence of 5:3:2
SP:SAMPLEPREP_SUMMARY            	MeOH:MeCN:water (v/v/v). The samples were spun down and the resulting
SP:SAMPLEPREP_SUMMARY            	supernatant was transferred to new tubes and dried under a vacuum. The resulting
SP:SAMPLEPREP_SUMMARY            	residue was reconstituted in 0.1% formic acid at a 3x concentration, then
SP:SAMPLEPREP_SUMMARY            	analyzed on a Thermo Vanquish UHPLC coupled to a Thermo Q Exactive MS as
SP:SAMPLEPREP_SUMMARY            	previously described in detail.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Negative ion Mode
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                     	95% water/5% acetonitrile; 1 mM ammonium acetate
CH:SOLVENT_B                     	95% acetonitrile/5% water; 1 mM ammonium acetate
CH:FLOW_GRADIENT                 	0-0.5 min 0% B, 0.5-1.1 min 0-100% B, 1.1-2.75 min hold at 100% B, 2.75-3 min
CH:FLOW_GRADIENT                 	100-0% B, 3-5 min hold at 0% B
CH:FLOW_RATE                     	0.450ml/min
CH:COLUMN_TEMPERATURE            	45
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms,
MS:MS_COMMENTS                   	microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV,
MS:MS_COMMENTS                   	capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas
MS:MS_COMMENTS                   	0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were
MS:MS_COMMENTS                   	annotated and integrated using Maven in conjunction with the KEGG database.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	Peak Areas
MS_METABOLITE_DATA_START
Samples	A	B	C	D	E	F
Factors	Factor:WT CART med | Sample source:Cells	Factor:WT CART med | Sample source:Cells	Factor:WT CART med | Sample source:Cells	Factor:MCJ KO CART med | Sample source:Cells	Factor:MCJ KO CART med | Sample source:Cells	Factor:MCJ KO CART med | Sample source:Cells
ATP	139159.47	170913.86	196101.25	229624.38	239588.77	212123.92
ADP	460100.28	321440.47	347160.09	561973.19	514727.5	558519.12
AMP	14696773	7411730.5	5901511.5	11825073	9307989	12111243
Guanosine	706371.5	583870.81	772630.19	651877.94	751452.19	1000826.25
Guanine	179010.77	192137.44	212885.33	199917.88	172953.22	211659.38
CTP	163354.23	155117.89	185706.33	214626.2	217024.14	255378.45
Inosine	1401242.12	1117825.62	1240428.38	1018568	1246078.12	1501443.12
Urate	2538730.25	910437.75	1245977.62	3304054	3013126	2129854.75
4-Pyridoxate	240387.02	124630.84	140313.17	264367.44	261100	278331.44
UDP-glucose	882831	1013224.5	1020436.5	1282072.5	1601022.62	952133.5
ADP-D-ribose	185038.61	112892.6	72200.15	83368.65	182623.33	162172.62
Flavin mononucleotide	136271.92	17141.96	55133.75	112020.66	119061.91	74165.75
Phosphate	87673848	86956008	94770056	69843016	79346256	85205240
Diphosphate	12571133	11159006	14998676	10029219	10777273	13078604
D-Glucose	1568506.62	1332253.5	1374051.12	1570285.62	1461848	1840128.88
D-Glyceraldehyde 3-phosphate/Glycerone phosphate	22737178	22080746	22010212	20847602	25759560	23411942
2/3-Phospho-D-glycerate	126825.31	36065.2	93441.79	80811.48	86920.93	134233.8
Pyruvate	1467146.38	753187.81	945885.25	2028017.62	1978371.12	1504044.5
Lactate	151183952	46993744	58135148	193258832	188688720	113521112
Maltose	163767.16	42327.64	68252.37	151615.56	156826.39	129142.88
Mannitol	973521.31	653739.44	836902.19	1196732.75	1001202.5	1060230.38
Citrate	1721370	514696.38	3115143	1689266.62	1185861.12	1532289.62
2-Oxoglutarate	196121.5	234366.7	323343.34	390385	368754.5	291902.72
Succinate	2060473.5	2083517	1757345.38	2301849.75	2229485.5	2361560.25
Fumarate	128623.55	71427.29	99814.27	191135.31	158932.5	121122.19
Malate	737415.69	313349.91	361115.84	787071.69	639734.5	638931.81
2-Hydroxyglutarate/Citramalate	649850.31	785034.5	807255.19	680504.25	822936.19	823706.31
Sedoheptulose 1-phosphate	1972689	2490104.75	2329230	2553944	2259548.75	2353439.25
alpha-D-Ribose 1-phosphate	303227.47	249294.44	247072.89	236807.62	247983	356669.84
Glutathione	39433228	36647368	36258580	50548148	53291796	52519536
S-Glutathionyl-L-cysteine	94909.62	110609.29	75721.62	115246.91	108462.25	141789.06
Dimethylglycine	270290.47	270398.66	268578.41	409909.16	403506.5	314898
N-Glycoloyl-neuraminate	4042426.25	4234706.5	4458959.5	6135506	4862716.5	4595501.5
UDP-N-acetyl-D-glucosamine	2857343.75	2416663.25	2524671	2507129.75	3704986.25	3425814.25
Phosphocreatine	190679.58	170025.55	183980	213917.77	208065.8	242989.69
N-Acetylornithine	84561.62	26509.86	36828.94	133748.45	131251.31	72074.24
Thiocysteine	33037.57	15142.17	43580.02	29794.14	28565.74	31926.61
Hexanoic acid (caproate)	951465	950341.44	1049168.88	1627820.62	1024610.56	1070548.62
Heptanoic acid	1187286.88	1200581.5	1390521.12	1891618.88	1512472.5	1342461.25
Octanoic acid (caprylate)	4484996	3851951.25	4811065.5	4691206.5	4378506.5	4653606.5
Nonanoic acid (pelargonate)	40871824	36044604	44527328	49873996	45871040	44914516
Decanoic acid (caprate)	18006338	16170040	16942330	15709861	19278966	22214190
Dodecanoic acid	11174421	11574391	10899474	10029879	12469247	11884756
Tetradecanoic acid	44788820	33189776	27799504	22755806	25780560	27756518
Hexadecanoic acid	148489632	113073344	115519552	77453728	78738520	93553928
Octadecanoic acid	2893985.25	3862629.25	3347352	3827461.75	3493608	3525607.75
Tetradecenoic acid	5203684.5	4409807.5	4073754.75	2057463	4869235	6195874.5
Hexadecenoic acid	54337036	42065228	33676548	18411496	22010606	31767574
Octadecenoic acid	38579036	26507568	19933766	11689092	15306057	22154814
Linoleate	8832487	5024178.5	4069594.75	1914747.12	2687335.25	3741257.25
Octadecatrienoic acid	539004.44	333771.31	233257.62	141170.89	223334.75	289780.53
Eicosatetraenoic acid	4374010.5	4493328.5	3179815	1033871.31	1690289.88	2761457.75
Docosahexaenoic acid	1147833.5	1244295.75	728014.94	429859	501239.34	826818.31
(8Z-11Z-14Z)-Icosatrienoic acid	927394.75	968999.56	617018.06	218943.58	374989.16	521112.16
(7Z-10Z-13Z-16Z-19Z)-Docosa-7-10-13-16-19-pentaenoic acid	1314551	1110387.25	771789.75	265715.78	413021.62	695086.94
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	CmpdID	parent	medRt
ATP	C00002	505.989	1.413
ADP	C00008	426.022	1.291
AMP	C00020	346.056	0.968
Guanosine	C00387	282.084	1.070
Guanine	C00242	150.041	0.920
CTP	C00063	481.978	0.610
Inosine	C00294	267.073	1.065
Urate	C00366	167.022	0.878
4-Pyridoxate	C00847	182.044	0.703
UDP-glucose	C00029	565.048	0.815
ADP-D-ribose	C01882	558.064	0.816
Flavin mononucleotide	C00061	455.102	0.705
Phosphate	C00009	96.970	0.607
Diphosphate	C00013	176.935	0.828
D-Glucose	C00031	179.056	0.684
D-Glyceraldehyde 3-phosphate/Glycerone phosphate	C00118	168.989	1.822
2/3-Phospho-D-glycerate	C00631	184.985	0.632
Pyruvate	C00022	87.009	0.764
Lactate	C01432	89.024	0.800
Maltose	C00208	341.109	0.708
Mannitol	C00392	181.070	0.928
Citrate	C00158	191.020	0.628
2-Oxoglutarate	C00026	145.014	0.739
Succinate	C00042	117.019	0.808
Fumarate	C00122	115.004	0.613
Malate	C00149	133.014	0.785
2-Hydroxyglutarate/Citramalate	C02630	147.030	0.919
Sedoheptulose 1-phosphate	C06222	289.033	0.633
alpha-D-Ribose 1-phosphate	C00620	229.012	0.639
Glutathione	C00051	306.078	0.795
S-Glutathionyl-L-cysteine	C05526	425.081	0.633
Dimethylglycine	C01026	102.056	0.621
N-Glycoloyl-neuraminate	C03410	324.094	0.642
UDP-N-acetyl-D-glucosamine	C00043	606.074	0.788
Phosphocreatine	C02305	210.029	0.601
N-Acetylornithine	C00437	173.093	0.915
Thiocysteine	C01962	151.986	0.785
Hexanoic acid (caproate)	C01585	115.076	1.938
Heptanoic acid	C17714	129.092	2.042
Octanoic acid (caprylate)	C06423	143.108	2.136
Nonanoic acid (pelargonate)	C01601	157.123	2.219
Decanoic acid (caprate)	C01571	171.139	2.302
Dodecanoic acid	C02679	199.170	2.497
Tetradecanoic acid	C06424	227.202	2.765
Hexadecanoic acid	C00249	255.233	3.169
Octadecanoic acid	C01530	283.264	2.168
Tetradecenoic acid	C08322	225.186	2.550
Hexadecenoic acid	C08362	253.217	2.831
Octadecenoic acid	C00712	281.249	3.219
Linoleate	C01595	279.233	2.929
Octadecatrienoic acid	C06427	277.217	2.669
Eicosatetraenoic acid	C00219	303.233	2.767
Docosahexaenoic acid	C06429	327.233	2.668
(8Z-11Z-14Z)-Icosatrienoic acid	C03242	305.249	2.930
(7Z-10Z-13Z-16Z-19Z)-Docosa-7-10-13-16-19-pentaenoic acid	C16513	329.249	2.795
METABOLITES_END
#END