#METABOLOMICS WORKBENCH cendalfr_20240411_071306 DATATRACK_ID:4769 STUDY_ID:ST003166 ANALYSIS_ID:AN005194 PROJECT_ID:PR001970
VERSION             	1
CREATED_ON             	April 11, 2024, 1:33 pm
#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                   	Metabolomics of Murine WT or MCJ KO CD19-BBz CD8 CAR-T cells
ST:STUDY_SUMMARY                 	MCJ/DnaJC15 is an endogenous negative regulator of Complex I and mitochondrial
ST:STUDY_SUMMARY                 	respiration. The goal of these experiments are to characterize the metabolic
ST:STUDY_SUMMARY                 	profile of murine WT or MCJ KO CD8 CD19-BBz CAR-T cells after 3 expansions (6
ST:STUDY_SUMMARY                 	days) with IL-2 (60IU/ml).
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           	-	WT CD19-BBz CART_1	factor:WT | Sample source:T-Cells	RAW_FILE_NAME(Raw File)=1
SUBJECT_SAMPLE_FACTORS           	-	WT CD19-BBz CART_2	factor:WT | Sample source:T-Cells	RAW_FILE_NAME(Raw File)=2
SUBJECT_SAMPLE_FACTORS           	-	WT CD19-BBz CART_3	factor:WT | Sample source:T-Cells	RAW_FILE_NAME(Raw File)=3
SUBJECT_SAMPLE_FACTORS           	-	WT CD19-BBz CART_4	factor:WT | Sample source:T-Cells	RAW_FILE_NAME(Raw File)=4
SUBJECT_SAMPLE_FACTORS           	-	MCJ KO CD19-BBz CART_1	factor:MCJ KO | Sample source:T-Cells	RAW_FILE_NAME(Raw File)=5
SUBJECT_SAMPLE_FACTORS           	-	MCJ KO CD19-BBz CART_2	factor:MCJ KO | Sample source:T-Cells	RAW_FILE_NAME(Raw File)=6
SUBJECT_SAMPLE_FACTORS           	-	MCJ KO CD19-BBz CART_3	factor:MCJ KO | Sample source:T-Cells	RAW_FILE_NAME(Raw File)=7
SUBJECT_SAMPLE_FACTORS           	-	MCJ KO CD19-BBz CART_4	factor:MCJ KO | Sample source:T-Cells	RAW_FILE_NAME(Raw File)=8
#COLLECTION
CO:COLLECTION_SUMMARY            	Mouse CD8 cells were isolated with negative selection as described above,
CO:COLLECTION_SUMMARY            	activated with anti-CD3/anti-CD28 beads (Dynabeads™ Mouse T-Activator CD3/CD28
CO:COLLECTION_SUMMARY            	for T-Cell Expansion and Activation, Gibco, Cat#11453D) with addition of
CO:COLLECTION_SUMMARY            	recombinant human IL-2 (rhIL-2) (60 IU/ml) and human recombinant IL-7 (10
CO:COLLECTION_SUMMARY            	ng/ml). On the second and third day of activation, the supernatant containing
CO:COLLECTION_SUMMARY            	the CD19-BBz CAR/hEGFR retrovirus was spun on a plate coated with retronectin
CO:COLLECTION_SUMMARY            	(Takara Bio Inc.) (2000xg for 2.5h at 32C). The activated cells were added to
CO:COLLECTION_SUMMARY            	the viral-coated plate for transduction. The transduced CD8 CAR-T cells were
CO:COLLECTION_SUMMARY            	removed from the beads on the fourth day and expanded with rhIL-2 (60 IU/ml) or
CO:COLLECTION_SUMMARY            	rhIL-7 (10 ng/ml) and rhL-15 (100 ng/ml). After 2 days (1st expansion) cells
CO:COLLECTION_SUMMARY            	were split 1/3 with fresh cytokine-containing medium. After 2 more days (2nd
CO:COLLECTION_SUMMARY            	expansion), cells were split again with fresh cytokine-containing medium. Two
CO:COLLECTION_SUMMARY            	days later (3rd expansion) cells were used for experiment or incubated in
CO:COLLECTION_SUMMARY            	cytokine free-medium. For CAR+ cells enrichment, the CAR-T cells expanded with
CO:COLLECTION_SUMMARY            	IL-2 for 3 expansions were incubated with an anti-hEGFR-PE (BioLegend,
CO:COLLECTION_SUMMARY            	Cat#352904, RRID: AB_10896794) antibody, followed by incubation with anti-PE
CO:COLLECTION_SUMMARY            	microbeads (Miltenyi, order#130-048-801), and purified using the Miltenyi LS
CO:COLLECTION_SUMMARY            	columns as recommended by the manufacturer (Miltenyi). The enrichment resulted
CO:COLLECTION_SUMMARY            	in a 98-100% CAR+ population, as verified by flow cytometry.
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 Area
MS_METABOLITE_DATA_START
Samples	WT CD19-BBz CART_1	WT CD19-BBz CART_2	WT CD19-BBz CART_3	WT CD19-BBz CART_4	MCJ KO CD19-BBz CART_1	MCJ KO CD19-BBz CART_2	MCJ KO CD19-BBz CART_3	MCJ KO CD19-BBz CART_4				
Factors	factor:WT | Sample source:T-Cells	factor:WT | Sample source:T-Cells	factor:WT | Sample source:T-Cells	factor:WT | Sample source:T-Cells	factor:MCJ KO | Sample source:T-Cells	factor:MCJ KO | Sample source:T-Cells	factor:MCJ KO | Sample source:T-Cells	factor:MCJ KO | Sample source:T-Cells
ATP	41731.19	6428.767	24878.19	35170.29	79503.05	81745.34	138619.4	85962.03				
CDP	53948	47685.77	46709.7	53225.76	83453.38	80334.26	79512.63	66829.29				
dTMP	11528.27	13090.34	15471.74	12250.69	8103.299	10143.27	9107.273	12798.74				
UTP	33895.8	14083.71	21179.4	29137.43	79893.7	80497.16	85839.19	48459.85				
4-Pyridoxate	53052.21	36336.4	38370.96	40768.04	53107.3	51397.92	67147.98	73606.19				
UDP-glucose	109945.5	102305	106772.5	117610.4	173604.3	171099.8	153633.5	137282.2				
ADP-D-ribose	80313.99	39212.17	48370.59	37083.43	26234.21	54659.27	40937.18	57243.11				
Phosphate	14296980	8234016	13455610	11907920	12452870	12267700	13097670	11994820				
Diphosphate	1350856	888204.6	1270134	1227957	1829761	1288761	1300646	1350158				
D-Glucose	34903.93	33176.79	52589.67	54858.92	37811.08	55359.25	37016.07	37469.9				
D-Glucose 6/1-phosphate	85955.66	67637.87	52940.54	77000.13	111030.3	77257.45	78838.41	79792.44				
D-Glyceraldehyde 3-phosphate/Glycerone phosphate	287686	343037.8	372692.3	339469.2	438925.6	401145.6	437910.4	360800.9				
2/3-Phospho-D-glycerate	20790.25	13434.66	14234.36	19509.62	38532.4	33113.87	25507.95	28076.16				
Pyruvate	57872.79	52969.32	45175.14	60090.41	53257.15	50325.11	74337.44	49558.11				
Lactate	4848126	3885394	5318762	5787558	5375694	5242856	6198282	5424948				
Maltose	21164.09	15210.54	15643.46	24864.53	10121.72	13867.65	27094.81	16564.82				
Mannitol/Sorbitol	40654.9	41214.98	40424.16	39911.29	52945.3	50903.8	36894.93	35577.58				
Citrate	618699.8	191719	289149.5	357374	404766.8	414949.8	642812.4	595414.9				
2-Oxoglutarate	12281.25	15227.17	15536.72	18042.83	28747.53	23252.08	33593.17	32512.49				
Succinate	138719.9	129564	173048.6	147926.4	174430.2	178328.8	205234.1	244900				
Fumarate	155572.1	90909.04	124985.8	130289.6	129184.5	166935.8	179206.8	177238.2				
Malate	328446.8	247421.1	218096.7	297673.4	325895.5	336860.8	453008.4	273032.2				
2-Hydroxyglutarate/Citramalate	39109.5	40886.45	46718.08	44507.89	74731.09	79205.07	82418.81	77209.23				
Sedoheptulose 1/7-phosphate	40664.46	38187.89	35360.77	34914.26	50929.48	34809.28	41409.61	46787.02				
alpha-D-Ribose 1-phosphate	169594.8	125331.4	116209	120834.6	142507.4	122830.7	135970.8	164456.7				
Dimethylglycine	183660.9	121348.4	160857.4	152375.3	145719	193498.6	185511.5	220374.2				
N-Acetylneuraminate	122704.1	62105.49	62626.44	68726.91	81198.21	100110.1	107409.4	115418.2				
N-Glycoloyl-neuraminate	249265.9	173564	179054.4	179983	232159.2	201731.4	225946.6	213605.1				
UDP-N-acetyl-D-glucosamine	229337.2	207586.8	248297.6	229223	367094	355713.3	327184.5	301008.9				
Phosphocreatine	12416.68	15688.38	12999.27	13079.56	20042.31	18910.34	17525.09	14660.42				
Sphinganine 1-phosphate	7634.625	6593.951	11418.5	9275.2	6087.835	6923.96	8480.534	9538.961				
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	CmpdID	parent	medRt
ATP	C00002	505.99	0.609
CDP	C00112	402.01	0.632
dTMP	C00364	321.05	0.929
UTP	C00075	482.96	0.630
4-Pyridoxate	C00847	182.04	0.716
UDP-glucose	C00029	565.05	0.620
ADP-D-ribose	C01882	558.06	0.646
Phosphate	C00009	96.97	0.670
Diphosphate	C00013	176.93	0.613
D-Glucose	C00031	179.06	0.691
D-Glucose 6/1-phosphate	C02965	259.02	0.637
D-Glyceraldehyde 3-phosphate/Glycerone phosphate	C00118	168.99	1.818
2/3-Phospho-D-glycerate	C00631	184.98	0.615
Pyruvate	C00022	87.01	0.811
Lactate	C01432	89.02	0.789
Maltose	C00208	341.11	0.729
Mannitol/Sorbitol	C00392	181.07	0.699
Citrate	C00158	191.02	0.627
2-Oxoglutarate	C00026	145.01	0.807
Succinate	C00042	117.02	0.808
Fumarate	C00122	108.24	0.628
Malate	C00149	133.01	0.612
2-Hydroxyglutarate/Citramalate	C02630	147.03	0.811
Sedoheptulose 1/7-phosphate	C06222	289.03	0.636
alpha-D-Ribose 1-phosphate	C00620	229.01	0.637
Dimethylglycine	C01026	102.05	0.639
N-Acetylneuraminate	C00270	308.10	0.646
N-Glycoloyl-neuraminate	C03410	324.09	0.643
UDP-N-acetyl-D-glucosamine	C00043	606.07	0.636
Phosphocreatine	C02305	210.03	0.622
Sphinganine 1-phosphate	C01120	380.26	3.706
METABOLITES_END
#END