#METABOLOMICS WORKBENCH juliehaines_20250807_085445 DATATRACK_ID:6260 STUDY_ID:ST004109 ANALYSIS_ID:AN006811 PROJECT_ID:PR002584
VERSION             	1
CREATED_ON             	August 8, 2025, 3:55 pm
#PROJECT
PR:PROJECT_TITLE                 	Serum metabolomics from WT and KRAS knockout mice
PR:PROJECT_SUMMARY               	We generated a clinically relevant animal model of cancer cachexia using an
PR:PROJECT_SUMMARY               	inducible, lung epithelial cell specific KrasG12D/+ (G12D) mice. Serum
PR:PROJECT_SUMMARY               	metabolomics was used alongside analyses of tumor, cellular, mutational, and
PR:PROJECT_SUMMARY               	transcriptomic characteristics to assess the degree to which this mouse model
PR:PROJECT_SUMMARY               	phenocopies human lung cancer cachexia.
PR:INSTITUTE                     	University of Colorado Anschutz Medical Campus
PR:LABORATORY                    	Lab of Angelo D'Alessandro in collaboration with lab of Michael Toth
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                   	Early adipose tissue wasting in a preclinical model of human lung cancer
ST:STUDY_TITLE                   	cachexia - Serum metabolomics from WT and KRAS knockout mice
ST:STUDY_SUMMARY                 	Cancer cachexia (CC), a syndrome of skeletal muscle and adipose wasting, reduces
ST:STUDY_SUMMARY                 	responsiveness to therapies and increases mortality. There are no approved
ST:STUDY_SUMMARY                 	treatments for CC, which may relate to discordance between pre-clinical models
ST:STUDY_SUMMARY                 	and human CC. To address the need for clinically relevant models of lung CC, we
ST:STUDY_SUMMARY                 	generated inducible, lung epithelial cell specific KrasG12D/+ (G12D) mice. G12D
ST:STUDY_SUMMARY                 	mice develop CC over a protracted time course and phenocopy tissue and tumor,
ST:STUDY_SUMMARY                 	cellular, mutational, transcriptomic, and metabolic characteristics of human
ST:STUDY_SUMMARY                 	lung CC. G12D mice demonstrate early loss of adipose, a phenotype that was
ST:STUDY_SUMMARY                 	apparent across numerous models of CC and translates to patients with lung
ST:STUDY_SUMMARY                 	cancer. Tumor-released factors promote adipocyte lipolysis, a driver of adipose
ST:STUDY_SUMMARY                 	wasting in CC, and adipose wasting was inversely related to tumor burden. Thus,
ST:STUDY_SUMMARY                 	G12D mice model key features of human lung CC and highlight a role for early
ST:STUDY_SUMMARY                 	tumor metabolic reprogramming of adipose tissue in CC.
ST:INSTITUTE                     	University of Colorado Anschutz Medical Campus
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
SU:GENDER                        	Not applicable
#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           	-	9	Sample source:serum | Genotype:WT	RAW_FILE_NAME(Raw file name)=DS1-68-001
SUBJECT_SAMPLE_FACTORS           	-	11	Sample source:serum | Genotype:WT	RAW_FILE_NAME(Raw file name)=DS1-68-002
SUBJECT_SAMPLE_FACTORS           	-	12	Sample source:serum | Genotype:WT	RAW_FILE_NAME(Raw file name)=DS1-68-003
SUBJECT_SAMPLE_FACTORS           	-	13	Sample source:serum | Genotype:WT	RAW_FILE_NAME(Raw file name)=DS1-68-004
SUBJECT_SAMPLE_FACTORS           	-	14	Sample source:serum | Genotype:WT	RAW_FILE_NAME(Raw file name)=DS1-68-005
SUBJECT_SAMPLE_FACTORS           	-	15	Sample source:serum | Genotype:WT	RAW_FILE_NAME(Raw file name)=DS1-68-006
SUBJECT_SAMPLE_FACTORS           	-	16	Sample source:serum | Genotype:KRAS	RAW_FILE_NAME(Raw file name)=DS1-68-007
SUBJECT_SAMPLE_FACTORS           	-	17	Sample source:serum | Genotype:KRAS	RAW_FILE_NAME(Raw file name)=DS1-68-008
SUBJECT_SAMPLE_FACTORS           	-	18	Sample source:serum | Genotype:KRAS	RAW_FILE_NAME(Raw file name)=DS1-68-009
SUBJECT_SAMPLE_FACTORS           	-	19	Sample source:serum | Genotype:KRAS	RAW_FILE_NAME(Raw file name)=DS1-68-010
SUBJECT_SAMPLE_FACTORS           	-	20	Sample source:serum | Genotype:KRAS	RAW_FILE_NAME(Raw file name)=DS1-68-011
#COLLECTION
CO:COLLECTION_SUMMARY            	All animal experiments were approved by the University of Vermont Institutional
CO:COLLECTION_SUMMARY            	Animal Care and Use Committee, in compliance with the National Institutes of
CO:COLLECTION_SUMMARY            	Health Guidelines for Use and Care of Laboratory Animals. Mice were housed with
CO:COLLECTION_SUMMARY            	sex-matched litter mates and given ad libitum access to standard chow and water,
CO:COLLECTION_SUMMARY            	except for a subset of mice that were housed singly to monitor food intake as
CO:COLLECTION_SUMMARY            	specified. Animals were allocated by genotype. G12D mice
CO:COLLECTION_SUMMARY            	(Scgb1a1-CreERTM-KrasLSL-G12D/+) were generated by crossing Scgb1a1-CreERTM mice
CO:COLLECTION_SUMMARY            	with KrasLSL-G12D/+ mice and were maintained on a mixed background. At 4-5
CO:COLLECTION_SUMMARY            	months of age, G12D or wild-type Scgb1a1-CreERTM (WT) littermates were
CO:COLLECTION_SUMMARY            	administered five consecutive daily intraperitoneal (IP) injections of 20 mg/ml
CO:COLLECTION_SUMMARY            	tamoxifen (Sigma-Aldrich, St. Louis, MO, USA) dissolved in corn oil at a dose of
CO:COLLECTION_SUMMARY            	1 mg tamoxifen/10 g body weight. Body weight was monitored 2-3 times weekly and
CO:COLLECTION_SUMMARY            	food intake was measured in a sub-group of individually housed mice for 6 weeks.
CO:COLLECTION_SUMMARY            	At 6- or 12-weeks post-tamoxifen injections, mice were euthanized by cervical
CO:COLLECTION_SUMMARY            	dislocation under pentobarbital anesthesia. Blood was collected by cardiac
CO:COLLECTION_SUMMARY            	puncture in serum separator tubes and centrifuged to isolate serum, aliquoted,
CO:COLLECTION_SUMMARY            	and stored at -80°C.
CO:SAMPLE_TYPE                   	Blood (serum)
#TREATMENT
TR:TREATMENT_SUMMARY             	No treatment, baseline (steady state) characterization only.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Serum specimens were thawed on ice then a 20 uL aliquot was mixed with 480 uL of
SP:SAMPLEPREP_SUMMARY            	ice cold 5:3:2 methanol:acetonitrile:water (v/v/v). Extraction was performed
SP:SAMPLEPREP_SUMMARY            	vigorous vortexing at 4°C followed by centrifugation for 10 min at 18,000 g at
SP:SAMPLEPREP_SUMMARY            	4°C. Extracts were transferred to autosampler vials (on ice) and analyzed
SP:SAMPLEPREP_SUMMARY            	immediately.
SP:PROCESSING_STORAGE_CONDITIONS 	4℃
SP:EXTRACT_STORAGE               	4℃
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Negative C18
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Thermo Vanquish
CH:COLUMN_NAME                   	Phenomenex Kinetex C18 (150 x 2.1 mm,1.7 µm)
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                     	450 µL/min
CH:COLUMN_TEMPERATURE            	45°C
CH:SAMPLE_INJECTION              	6 µL
#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	9	11	12	13	14	15	16	17	18	19	20
Factors	Sample source:serum | Genotype:WT	Sample source:serum | Genotype:WT	Sample source:serum | Genotype:WT	Sample source:serum | Genotype:WT	Sample source:serum | Genotype:WT	Sample source:serum | Genotype:WT	Sample source:serum | Genotype:KRAS	Sample source:serum | Genotype:KRAS	Sample source:serum | Genotype:KRAS	Sample source:serum | Genotype:KRAS	Sample source:serum | Genotype:KRAS
GMP	0	0	0	2658709	4410348	6045331	0	0	941164	0	0
Cytidine	661220	1307945	578834	394911	553362	407572	700059	555075	339679	333789	529020
UMP	0	0	0	1332730	2861873	3951522	0	0	339981	0	0
IMP	0	0	0	218903	1054279	1309427	0	0	73699	0	0
Inosine	26985	26817	139417	94222	868385	1138166	50021	9233	15068	13784	15058
2',3'-Cyclic CMP	28505	21721	23004	158717	21505	29309	22748	23678	8202	10373	11496
Pyridoxal	32305	37164	51043	45895	26933	13920	49044	32497	22026	31301	38980
ADP-D-ribose	174270	264597	713793	148727	18687	65480	692455	165467	87619	785831	825400
Diphosphate	5058484	4140828	4657018	4405589	3355443	4313003	10228182	9465898	11941410	13308042	12470230
D-Glucose	10797245	12710238	15790108	10086266	16669657	14542549	10474954	10639797	10500682	8217481	8120780
D-Glucose 6-phosphate	3050829	7598239	4111653	2484233	3707226	3332467	6367036	3194843	4611498	5614424	3945977
D-Glyceraldehyde 3-phosphate/Glycerone phosphate	271478	969559	449890	449034	829015	1028560	593034	251204	804414	679420	430455
2/3-Phospho-D-glycerate	383030	604974	398831	660285	325791	329261	710231	504182	851615	996292	702263
Maltose	48640	103141	58207	192794	60015	67655	37683	54784	77157	35538	56057
Mannitol	158153	235047	219627	456862	199991	238794	229409	272123	261030	306191	246018
D-Rhamnose	203216	166552	174661	670339	246725	113617	295408	231419	333006	138021	278459
Citrate	140835712	143947088	144756560	370016096	123095376	132060536	120359920	149673696	96995448	119774608	125277816
D-Erythrose 4-phosphate	133408	358392	140710	60865	142831	121788	285136	172069	183693	202123	178071
Sedoheptulose 1-phosphate	144202	2155333	160137	59830	140088	62847	702284	74776	883868	471611	507352
alpha-D-Ribose 1-phosphate	2221391	8609773	2151598	6067022	6672979	5778801	3766752	1673389	10946284	2973170	2987065
Glutathione disulfide	596953	660797	1841012	227706	2896232	1839024	2488018	1240301	1811669	2545036	1484834
S-Glutathionyl-L-cysteine	3723906	3623893	6919137	2573970	8366855	7392783	6341924	5645688	5096081	7427528	5834972
Ascorbate	26768866	1603550	42108020	71538880	38476912	28185480	28209626	34208676	33993532	49824352	1554404
Dehydroascorbate	6273661	6175855	6410750	19332312	5396581	5437989	5192712	6655833	4347518	5467976	5275782
5-L-Glutamyl-taurine	95088	166667	128474	687599	112467	84382	143772	43347	152176	178820	91862
Argininosuccinate	56467	124391	90798	120019	203099	61096	105301	37420	49504	99083	69220
N-Acetylneuraminate	662364	763846	668114	1583283	575362	575217	679415	601956	471991	552406	551483
N-Glycoloyl-neuraminate	550176	549430	585442	2779158	822775	613838	749204	692148	871828	778744	725317
alpha-D-Glucosamine 1-phosphate	90944	172116	138808	254190	98092	92640	170033	104704	73203	92189	96599
CMP-N-acetylneuraminate	19871	42621	134046	6279	265112	143230	219571	94102	150564	212499	109054
N-Acetyl-L-citrulline	64771	111019	87131	424924	40693	27326	85463	59876	14301	76331	64430
Pantothenate	342917	370859	322604	335355	170255	117134	284975	381658	123153	264669	240152
3-Sulfino-L-alanine	173445	281301	51051	597986	91827	136520	131453	91416	47340	49531	35288
3-Sulfocatechol	546121	1542517	1339054	7884237	383560	614702	786590	856455	360728	565018	804558
Indole-3-acetate	17497	18179	25591	70404	10532	10077	20547	22407	6383	20841	19121
Indolepyruvate	99349	174168	226563	622311	72061	44003	132830	147365	51173	114844	114786
g-Oxalo-crotonate	44708	63482	37486	314112	123320	34689	147594	170709	93099	123243	23064
3D-(3-5/4)-Trihydroxycyclohexane-1-2-dione	675785	794432	1422355	3182986	945711	670785	1233542	1380020	821090	636845	732745
Glycerol 3-phosphate	6377553	6332681	12228423	6306976	14433789	10898623	9550730	6941035	8085534	11591325	6904841
Nonanoic acid (pelargonate)	4950537	4590237	5007635	3234921	2374136	2189784	5863629	4306902	1834099	3898971	3948578
Decanoic acid (caprate)	2093639	1862451	1704451	1308158	1225362	1138831	1971475	1595255	855428	1526923	1647285
Dodecanoic acid (lauric acid)	1896382	1811871	1627245	1254528	1219683	1096037	2196231	1486266	803543	1395598	1563173
Tetradecanoic acid (myristic acid)	7388319	9646253	9184717	7117964	5800317	4721814	8512757	8735619	4751046	8072865	7156985
Hexadecanoic acid (palmitic acid)	303848896	274356576	262766336	217305568	196881264	185374416	277857600	248603520	198317456	180654880	252390512
Octadecanoic acid (stearic acid)	251273920	196802240	146211696	114185792	130293568	167296464	223637568	180728144	143610704	96982056	156121488
Tetradecenoic acid (myristoleic acid)	767309	699849	664328	506909	685239	517646	685075	840240	457735	746725	637531
Hexadecenoic acid (Palmitoleic acid)	23860058	27101192	28864366	26143436	30942836	18149106	14895680	25551482	16973738	20139886	16925320
Octadecenoic acid (Oleic acid)	152013744	155324384	155483152	122755712	137840688	101307728	129745704	152066352	140655248	126913104	129599024
Linoleic acid ((9Z,12Z)-Octadecadienoic acid)	131791056	116464520	114889264	116795800	113444840	88559304	138973232	141866752	123881664	116009264	124641240
a-Linolenic acid (Octadecatrienoic acid)	8821786	10739901	8556023	9303521	8848646	7132622	10107186	11375326	10142776	10642493	8369298
Arachidonic acid (Eicosatetraenoic acid)	16009761	11286264	11977697	14281042	11226578	8379012	14484015	17396314	12206515	12021023	15664829
Docosahexaenoic acid	16940302	13491442	13132160	16695275	16575421	12738201	21883068	24802502	19536236	19071830	25009188
Dodecanedioic acid	1601065	1539408	1869643	1531964	1079590	1159823	1784641	1395544	1043316	1365221	1174490
Eicosapentaenoic acid	5685737	4536875	5541251	5390781	4947356	3280912	4972833	5627899	5689976	4715223	5475572
(8Z-11Z-14Z)-Icosatrienoic acid	2619161	2939523	2420653	3248677	2832528	1928381	2576096	3069513	2402929	2313813	2690873
(7Z-10Z-13Z-16Z-19Z)-Docosa-7-10-13-16-19-pentaenoic acid	2596363	2649333	2635199	2837139	2939139	1810650	2348728	2443384	2560049	2171005	2077935
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	KEGG ID	m/z	r.t.
GMP	C00144	362.050171	0.629
Cytidine	C00475	242.078522	0.652
UMP	C00105	323.027832	0.63
IMP	C00130	347.039215	0.649
Inosine	C00294	267.072876	0.689
2',3'-Cyclic CMP	C02354	304.032837	0.675
Pyridoxal	C00250	166.04953	0.695
ADP-D-ribose	C01882	558.063049	0.585
Diphosphate	C00013	176.934616	0.615
D-Glucose	C00031	179.05481	0.67
D-Glucose 6-phosphate	C02965	259.021729	0.607
D-Glyceraldehyde 3-phosphate/Glycerone phosphate	C00118	168.989273	0.625
2/3-Phospho-D-glycerate	C00631	184.98439	0.589
Maltose	C00208	341.108246	0.679
Mannitol	C00392	181.070526	0.668
D-Rhamnose	C01684	163.059845	0.66
Citrate	C00158	191.018433	0.612
D-Erythrose 4-phosphate	C00279	199.000031	0.62
Sedoheptulose 1-phosphate	C06222	289.03183	0.619
alpha-D-Ribose 1-phosphate	C00620	229.010956	0.618
Glutathione disulfide	C00127	611.143494	0.574
S-Glutathionyl-L-cysteine	C05526	425.079773	0.611
Ascorbate	C00072	175.023483	0.632
Dehydroascorbate	C05422	173.007797	0.62
5-L-Glutamyl-taurine	C05844	253.050034	1.898
Argininosuccinate	C03406	289.114685	0.622
N-Acetylneuraminate	C00270	308.098145	0.634
N-Glycoloyl-neuraminate	C03410	324.092865	0.637
alpha-D-Glucosamine 1-phosphate	C06156	258.03775	0.617
CMP-N-acetylneuraminate	C00128	613.140503	0.577
N-Acetyl-L-citrulline	C15532	216.0979	0.652
Pantothenate	C00864	218.102402	0.678
3-Sulfino-L-alanine	C00606	152.000839	0.635
3-Sulfocatechol	C06336	188.985077	0.684
Indole-3-acetate	C00954	174.054794	1.759
Indolepyruvate	C00331	202.049896	1.75
g-Oxalo-crotonate	C03453	157.013092	0.637
3D-(3-5/4)-Trihydroxycyclohexane-1-2-dione	C04287	159.028458	0.627
Glycerol 3-phosphate	C00093	171.00499	0.619
Nonanoic acid (pelargonate)	C01601	157.121948	2.131
Decanoic acid (caprate)	C01571	171.137695	2.21
Dodecanoic acid (lauric acid)	C02679	199.169174	2.37
Tetradecanoic acid (myristic acid)	C06424	227.200684	2.643
Hexadecanoic acid (palmitic acid)	C00249	255.232162	3.033
Octadecanoic acid (stearic acid)	C01530	283.26355	3.632
Tetradecenoic acid (myristoleic acid)	C08322	225.185089	2.43
Hexadecenoic acid (Palmitoleic acid)	C08362	253.216537	2.684
Octadecenoic acid (Oleic acid)	C00712	281.247833	3.071
Linoleic acid ((9Z,12Z)-Octadecadienoic acid)	C01595	279.232147	2.735
a-Linolenic acid (Octadecatrienoic acid)	C06427	277.216583	2.522
Arachidonic acid (Eicosatetraenoic acid)	C00219	303.23233	2.629
Docosahexaenoic acid	C06429	327.23233	2.531
Dodecanedioic acid	C02678	229.143646	1.896
Eicosapentaenoic acid	C06428	301.216644	2.465
(8Z-11Z-14Z)-Icosatrienoic acid	C03242	305.248016	2.812
(7Z-10Z-13Z-16Z-19Z)-Docosa-7-10-13-16-19-pentaenoic acid	C16513	329.248352	2.644
METABOLITES_END
#END