#METABOLOMICS WORKBENCH Jung_DNLI_20240919_115027 DATATRACK_ID:5207 STUDY_ID:ST003501 ANALYSIS_ID:AN005747 PROJECT_ID:PR002147
VERSION             	1
CREATED_ON             	September 26, 2024, 4:43 pm
#PROJECT
PR:PROJECT_TITLE                 	TREM2 expression level is critical for microglial state, metabolic capacity and
PR:PROJECT_TITLE                 	efficacy of TREM2 agonism
PR:PROJECT_TYPE                  	Preclinical Mouse study
PR:PROJECT_SUMMARY               	Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator
PR:PROJECT_SUMMARY               	of microglial activity and sequence variants are major risk factors for late
PR:PROJECT_SUMMARY               	onset Alzheimer’s disease (LOAD). To better understand the molecular and
PR:PROJECT_SUMMARY               	functional changes associated with TREM2 signalling, we generated a TREM2
PR:PROJECT_SUMMARY               	reporter mouse model and observed a gradual upregulation of reporter expression
PR:PROJECT_SUMMARY               	with increasing plaque proximity. Isolated microglia were sorted based on
PR:PROJECT_SUMMARY               	reporter expression and their transcriptomic profiles acquired in both wildtype
PR:PROJECT_SUMMARY               	and APP transgenic animals, allowing us to disentangle TREM2 versus
PR:PROJECT_SUMMARY               	pathology-specific effects. Bulk RNA sequencing highlighted TREM2
PR:PROJECT_SUMMARY               	level-dependent changes in major immunometabolic pathways, with enrichment of
PR:PROJECT_SUMMARY               	genes in oxidative phosphorylation and cholesterol metabolism in microglia with
PR:PROJECT_SUMMARY               	increased TREM2 expression. To confirm these findings, we next analysed uptake
PR:PROJECT_SUMMARY               	of fluorodeoxyglucose (FDG) and examined metabolomic and lipidomic profiles.
PR:PROJECT_SUMMARY               	Again, independent of Aβ pathology, TREM2 expression correlated with uptake of
PR:PROJECT_SUMMARY               	FDG as well as increased cellular redox, energetics, and cholesterol
PR:PROJECT_SUMMARY               	homeostasis. Finally, we performed chronic treatment with a brain penetrant
PR:PROJECT_SUMMARY               	TREM2 agonist and identified a window of TREM2 expression where microglia are
PR:PROJECT_SUMMARY               	most responsive. Thus, our data provide novel insights into TREM2-mediated
PR:PROJECT_SUMMARY               	regulation of microglial metabolic function and informs current efforts to bring
PR:PROJECT_SUMMARY               	TREM2 agonists into clinical application.
PR:INSTITUTE                     	Denali Therapeutics
PR:DEPARTMENT                    	Development Sciences
PR:LAST_NAME                     	Suh
PR:FIRST_NAME                    	Jung
PR:ADDRESS                       	161 Oyster Point Blvd, South San Francisco, California, 94080, USA
PR:EMAIL                         	suh@dnli.com
PR:PHONE                         	+1 6507973837
PR:FUNDING_SOURCE                	Denali Therapeutics
PR:PUBLICATIONS                  	https://www.biorxiv.org/content/10.1101/2024.07.18.604115v1
#STUDY
ST:STUDY_TITLE                   	TREM2 expression level is critical for microglial state, metabolic capacity and
ST:STUDY_TITLE                   	efficacy of TREM2 agonism
ST:STUDY_SUMMARY                 	Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator
ST:STUDY_SUMMARY                 	of microglial activity and sequence variants are major risk factors for late
ST:STUDY_SUMMARY                 	onset Alzheimer’s disease (LOAD). To better understand the molecular and
ST:STUDY_SUMMARY                 	functional changes associated with TREM2 signalling, we generated a TREM2
ST:STUDY_SUMMARY                 	reporter mouse model and observed a gradual upregulation of reporter expression
ST:STUDY_SUMMARY                 	with increasing plaque proximity. Isolated microglia were sorted based on
ST:STUDY_SUMMARY                 	reporter expression and their transcriptomic profiles acquired in both wildtype
ST:STUDY_SUMMARY                 	and APP transgenic animals, allowing us to disentangle TREM2 versus
ST:STUDY_SUMMARY                 	pathology-specific effects. Bulk RNA sequencing highlighted TREM2
ST:STUDY_SUMMARY                 	level-dependent changes in major immunometabolic pathways, with enrichment of
ST:STUDY_SUMMARY                 	genes in oxidative phosphorylation and cholesterol metabolism in microglia with
ST:STUDY_SUMMARY                 	increased TREM2 expression. To confirm these findings, we next analysed uptake
ST:STUDY_SUMMARY                 	of fluorodeoxyglucose (FDG) and examined metabolomic and lipidomic profiles.
ST:STUDY_SUMMARY                 	Again, independent of Aβ pathology, TREM2 expression correlated with uptake of
ST:STUDY_SUMMARY                 	FDG as well as increased cellular redox, energetics, and cholesterol
ST:STUDY_SUMMARY                 	homeostasis. Finally, we performed chronic treatment with a brain penetrant
ST:STUDY_SUMMARY                 	TREM2 agonist and identified a window of TREM2 expression where microglia are
ST:STUDY_SUMMARY                 	most responsive. Thus, our data provide novel insights into TREM2-mediated
ST:STUDY_SUMMARY                 	regulation of microglial metabolic function and informs current efforts to bring
ST:STUDY_SUMMARY                 	TREM2 agonists into clinical application.
ST:INSTITUTE                     	Denali Therapeutics
ST:LAST_NAME                     	Suh
ST:FIRST_NAME                    	Jung
ST:ADDRESS                       	161 Oyster Point Blvd, South San Francisco, California, 94080, USA
ST:EMAIL                         	suh@dnli.com
ST:PHONE                         	+1 6507973837
ST:NUM_GROUPS                    	5
ST:TOTAL_SUBJECTS                	26
ST:NUM_MALES                     	26
ST:STUDY_COMMENTS                	Release as soon as it is possible
ST:PUBLICATIONS                  	https://www.biorxiv.org/content/10.1101/2024.07.18.604115v1
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
SU:AGE_OR_AGE_RANGE              	15 mo
SU:GENDER                        	Male
#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           	Pool_1	HSA-000019615	genotype:NA | condition:NA | group:NA | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_002; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_001; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_002; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_002
SUBJECT_SAMPLE_FACTORS           	2_59_mid_WT	HSA-000019571	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_003; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_009; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_003; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_003
SUBJECT_SAMPLE_FACTORS           	12_63_mid_WT	HSA-000019581	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_004; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_027; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_004; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_004
SUBJECT_SAMPLE_FACTORS           	24_78_low_APP	HSA-000019593	genotype:APP | condition:low | group:low_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_005; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_017; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_005; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_005
SUBJECT_SAMPLE_FACTORS           	10_62_mid_WT	HSA-000019579	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_006; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_016; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_006; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_006
SUBJECT_SAMPLE_FACTORS           	15_69_low_WT	HSA-000019584	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_007; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_022; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_007; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_007
SUBJECT_SAMPLE_FACTORS           	25_78_mid_APP	HSA-000019594	genotype:APP | condition:mid | group:mid_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_008; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_012; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_008; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_008
SUBJECT_SAMPLE_FACTORS           	18_74_mid_APP	HSA-000019587	genotype:APP | condition:mid | group:mid_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_009; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_003; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_009; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_009
SUBJECT_SAMPLE_FACTORS           	17_74_low_APP	HSA-000019586	genotype:APP | condition:low | group:low_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_010; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_004; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_010; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_010
SUBJECT_SAMPLE_FACTORS           	8_61_high_APP	HSA-000019577	genotype:APP | condition:high | group:high_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_011; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_011; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_011; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_011
SUBJECT_SAMPLE_FACTORS           	21_76_mid_WT	HSA-000019590	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_012; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_020; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_012; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_012
SUBJECT_SAMPLE_FACTORS           	14_65_mid_WT	HSA-000019583	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_013; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_028; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_013; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_013
SUBJECT_SAMPLE_FACTORS           	7_61_mid_APP	HSA-000019576	genotype:APP | condition:mid | group:mid_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_014; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_023; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_014; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_014
SUBJECT_SAMPLE_FACTORS           	1_59_low_WT	HSA-000019570	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_015; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_026; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_015; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_015
SUBJECT_SAMPLE_FACTORS           	5_60_high_APP	HSA-000019574	genotype:APP | condition:high | group:high_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_016; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_007; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_016; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_016
SUBJECT_SAMPLE_FACTORS           	22_77_low_WT	HSA-000019591	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_017; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_010; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_017; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_017
SUBJECT_SAMPLE_FACTORS           	Pool_2	HSA-000019616	genotype:NA | condition:NA | group:NA | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_018; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_014; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_018; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_018
SUBJECT_SAMPLE_FACTORS           	23_77_mid_WT	HSA-000019592	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_019; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_015; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_019; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_019
SUBJECT_SAMPLE_FACTORS           	11_63_low_WT	HSA-000019580	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_020; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_019; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_020; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_020
SUBJECT_SAMPLE_FACTORS           	3_60_low_APP	HSA-000019572	genotype:APP | condition:low | group:low_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_021; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_008; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_021; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_021
SUBJECT_SAMPLE_FACTORS           	26_78_high_APP	HSA-000019595	genotype:APP | condition:high | group:high_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_022; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_025; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_022; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_022
SUBJECT_SAMPLE_FACTORS           	19_74_high_APP	HSA-000019588	genotype:APP | condition:high | group:high_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_023; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_013; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_023; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_023
SUBJECT_SAMPLE_FACTORS           	9_62_low_WT	HSA-000019578	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_024; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_002; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_024; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_024
SUBJECT_SAMPLE_FACTORS           	6_61_low_APP	HSA-000019575	genotype:APP | condition:low | group:low_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_025; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_021; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_025; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_025
SUBJECT_SAMPLE_FACTORS           	20_76_low_WT	HSA-000019589	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_026; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_024; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_026; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_026
SUBJECT_SAMPLE_FACTORS           	4_60_mid_APP	HSA-000019573	genotype:APP | condition:mid | group:mid_disease | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_027; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_006; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_027; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_027
SUBJECT_SAMPLE_FACTORS           	13_65_low_WT	HSA-000019582	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_028; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_018; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_028; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_028
SUBJECT_SAMPLE_FACTORS           	16_69_mid_WT	HSA-000019585	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_029; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_005; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_029; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_029
SUBJECT_SAMPLE_FACTORS           	Pool_3	HSA-000019617	genotype:NA | condition:NA | group:NA | Sample source:microglia	RAW_FILE_NAME(Raw Source Name.LP)=20220209_BL_HEX-000330_Lipid_Pos_030; RAW_FILE_NAME(Raw Source Name.TG)=20220324_BL_HEX-000330_TGs_Pos_029; RAW_FILE_NAME(Raw Source Name.MP)=20220209_BL_HEX-000330_Met_Pos_030; RAW_FILE_NAME(Raw Source Name.MN)=20220211_BL_HEX-000330_Met_Neg_030
#COLLECTION
CO:COLLECTION_SUMMARY            	Microglia isolation was performed using the Magnetic-activated cell sorting
CO:COLLECTION_SUMMARY            	(MACS) system (Miltenyi Biotec). No CD11b enrichment step was performed as the
CO:COLLECTION_SUMMARY            	intrinsic mKate2 reporter is only expressed in TREM2 expressing (microglia)
CO:COLLECTION_SUMMARY            	cells. Hence, fluorescence-activated cell sorting was performed based on the
CO:COLLECTION_SUMMARY            	mKate2 fluorescence signal and sorted into low, mid and high expressing
CO:COLLECTION_SUMMARY            	subpopulations, as a proxy for the TREM2 expression of individual cells.
CO:SAMPLE_TYPE                   	microglia
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	No treatment
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Pellets from the sorted subpopulations were reconstituted on ice in 9:1
SP:SAMPLEPREP_SUMMARY            	MeOH:water including internal standards, vortexed for 1 minute, and spun down
SP:SAMPLEPREP_SUMMARY            	for 5 minutes at 10,000 g. Supernatant was transferred to glass vial for
SP:SAMPLEPREP_SUMMARY            	analysis by LC-MS.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	For each analysis, 5 µL of sample was injected on a BEH C18 1.7 µm, 2.1×100
CH:CHROMATOGRAPHY_SUMMARY        	mm column (Waters) using a flow rate of 0.25 mL/min at 55°C. For positive
CH:CHROMATOGRAPHY_SUMMARY        	ionization mode, mobile phase A consisted of 60:40 acetonitrile/water (v/v) with
CH:CHROMATOGRAPHY_SUMMARY        	10 mM ammonium formate + 0.1% formic acid; mobile phase B consisted of
CH:CHROMATOGRAPHY_SUMMARY        	90:10 isopropyl alcohol/acetonitrile (v/v) with 10 mM ammonium formate +
CH:CHROMATOGRAPHY_SUMMARY        	0.1% formic acid. The gradient was programmed as follows: 0.0-8.0 min from 45% B
CH:CHROMATOGRAPHY_SUMMARY        	to 99% B, 8.0-9.0 min at 99% B, 9.0-9.1 min to 45% B, and 9.1-10.0 min at 45% B.
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Agilent 1290 Infinity II
CH:COLUMN_NAME                   	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
CH:SOLVENT_A                     	60% acetonitrile/40% water; 10 mM ammonium formate; 0.1% formic acid
CH:SOLVENT_B                     	90% isopropyl alcohol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic
CH:SOLVENT_B                     	acid
CH:FLOW_GRADIENT                 	0.0-8.0 min from 45% B to 99% B, 8.0-9.0 min at 99% B, 9.0-9.1 min to 45% B, and
CH:FLOW_GRADIENT                 	9.1-10.0 min at 45% B.
CH:FLOW_RATE                     	0.25 mL/min
CH:COLUMN_TEMPERATURE            	55
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	ABI Sciex 6500+ Qtrap
MS:INSTRUMENT_TYPE               	Triple quadrupole
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	Curtain gas at 40 psi (positive mode); collision gas was set at medium; ion
MS:MS_COMMENTS                   	spray voltage at 5500 V (positive mode); temperature at 250°C (positive mode);
MS:MS_COMMENTS                   	ion source Gas 1 at 55 psi; ion source Gas 2 at 60 psi; entrance potential at 10
MS:MS_COMMENTS                   	V (positive mode); and  collision cell exit potential at 12.5 V (positive
MS:MS_COMMENTS                   	mode). Quantification was performed using MultiQuant 3.02 (Sciex). Increased
MS:MS_COMMENTS                   	MRM dwell time for specific list of TG transitions.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	log2(area)
MS_METABOLITE_DATA_START
Samples	HSA-000019615	HSA-000019578	HSA-000019587	HSA-000019586	HSA-000019585	HSA-000019573	HSA-000019574	HSA-000019572	HSA-000019571	HSA-000019591	HSA-000019577	HSA-000019594	HSA-000019588	HSA-000019616	HSA-000019592	HSA-000019579	HSA-000019593	HSA-000019582	HSA-000019580	HSA-000019590	HSA-000019575	HSA-000019584	HSA-000019576	HSA-000019589	HSA-000019595	HSA-000019570	HSA-000019581	HSA-000019583	HSA-000019617
Factors	genotype:NA | condition:NA | group:NA | Sample source:microglia	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	genotype:APP | condition:mid | group:mid_disease | Sample source:microglia	genotype:APP | condition:low | group:low_disease | Sample source:microglia	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	genotype:APP | condition:mid | group:mid_disease | Sample source:microglia	genotype:APP | condition:high | group:high_disease | Sample source:microglia	genotype:APP | condition:low | group:low_disease | Sample source:microglia	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	genotype:APP | condition:high | group:high_disease | Sample source:microglia	genotype:APP | condition:mid | group:mid_disease | Sample source:microglia	genotype:APP | condition:high | group:high_disease | Sample source:microglia	genotype:NA | condition:NA | group:NA | Sample source:microglia	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	genotype:APP | condition:low | group:low_disease | Sample source:microglia	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	genotype:APP | condition:low | group:low_disease | Sample source:microglia	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	genotype:APP | condition:mid | group:mid_disease | Sample source:microglia	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	genotype:APP | condition:high | group:high_disease | Sample source:microglia	genotype:WT | condition:low | group:low_healthy | Sample source:microglia	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	genotype:WT | condition:mid | group:mid_healthy | Sample source:microglia	genotype:NA | condition:NA | group:NA | Sample source:microglia
TG(15:0/18:1(d7)/15:0)	25.243380773845725	25.545994421807624	25.68254143323414	25.547517927489803	25.58783500794844	25.673804478314135	25.40194020759608	25.723188638751697	25.83602602002024	25.83080887452497	25.435375775042015	25.739616639088034	25.354552647807935	25.19728703	25.626068332194652	25.746764761454134	25.27543089387998	25.61492623853068	25.487856025057585	25.74512041579826	25.77908316699115	25.787109557754327	25.39701160419942	25.44527810896745	25.72294080295821	25.82103696223319	25.365012102650034	25.677706454279864	25.146376181807586
TG(18:0_36:2)	14.096601163640505	13.808592682358379	13.962435139218597	14.431670212599975	14.235840888026557	13.74845829759845	14.523704592112724	14.070769792388761	14.734617935029663	14.352071370040493	14.704940955731495	14.069850819386712	14.004508647452846	14.04860695517222	14.083781603321036	13.967103600256783	14.019164897032885	13.81060709243869	14.025928885873592	14.941128556132645	13.701274747116548	13.859600017811006	13.93305899249931	14.142237221069315	14.541697658939414	13.888299119645241	14.378719626405601	14.033872241327696	13.825149249981658
TG(18:1_34:2)	14.575982894279898	14.256911450169738	14.372771033255711	14.509444154538143	14.992772366055863	14.074530460550271	14.801404494820245	14.158826463357114	14.854911999099139	14.963229317636669	15.148953628968005	14.381957399065751	14.448638634063508	14.224153088699584	14.527820250396475	13.87595076205404	14.332295092133135	14.215737860271354	14.334594584199413	16.518808977611855	14.051907145343003	14.298665774508411	14.045403413155563	14.809734666091584	14.531973466039048	13.91897557552019	13.75175719349013	14.725573001340809	14.368437250532663
TG(18:1_34:3)	10.809966730484227	10.717761299357445	11.477551606373659	11.14671812612507	11.675135201064204	11.15603803443876	11.700306828725772	11.031850225285009	11.267945213847513	12.004220289756182	12.040516262415535	11.101291995150568	11.77765361828471	10.91418612862707	11.684361677038378	10.375493043821209	11.284424805305907	10.822450214184192	11.070562114499205	14.144983335378699	10.900988742512652	11.332162500033203	10.643932795372391	11.855827113730586	11.213808770715033	10.117809589806402	10.664991257541253	11.369551147538495	11.035648409789891
TG(20:4_32:1)	10.397902610183431	9.586539723311551	11.603658904858632	10.68382501207869	10.583359211274386	10.509895793544812	11.633990365378743	10.698040514825026	9.879913596	10.467906589486946	11.45175679827452	12.590082382872776	11.521473394090076	10.249934949176815	10.796612574787634	9.085887593895656	8.263076150587908	10.412509374525555	9.428780556452963	11.725195461448154	11.170129700129612	10.758278007869333	10.53630732395444	11.040741657044101	12.344457592615276	10.078802949606645	9.345458721129376	11.26703403653087	10.62791667
TG(20:4_34:2)	NA	9.491485018	10.440534310849023	9.446054651967142	10.469903794842628	9.857314056	10.912349701364947	10.392460637859124	9.482517207729167	11.071681603867411	10.749819626977258	11.410790472416583	10.749695468153408	9.695815162020489	10.095069051949132	9.306340743812555	9.890000919	10.586016542803808	9.013414984351103	10.274946157225953	10.37338658535528	10.626356576064767	10.268706051819539	10.862739422753362	10.996602061871146	10.304405518669801	8.299820241690208	10.816728879912956	9.600770965025204
TG(20:4_34:3)	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
TG(20:4_36:0)	9.696037008987416	NA	10.442148501275435	8.926756612098112	10.673452664040278	9.377291418786621	11.201804282365101	9.149501802383426	10.347861530497847	10.211372052585869	9.842671323933542	10.99872085828857	10.845391968613384	10.033252903330979	10.537966817504529	10.389075276380256	8.856353606953979	NA	8.968220351053098	10.14157175279787	9.763520065765555	10.30700705429515	9.090558684241136	9.425700164804816	11.001368092380437	9.580760269345184	8.802886336124423	10.766246104560249	9.600127114175804
TG(20:4_36:2)	10.256419124927431	10.15765828401578	11.676519831196385	10.537159211836453	10.859836463862393	10.053801050936574	12.280014941401756	11.091625647789302	10.924319388150604	12.031099348975305	11.47237204951044	12.246541624153718	11.819960573641271	10.836460006452272	10.210947253333043	10.486959050068512	10.186250930667649	10.262250634547499	10.274730144699701	11.19597614495817	11.184892425840411	11.056039943439899	10.673355604195088	11.350035203804227	12.352592970394532	10.37691613979057	9.889469735287985	11.582341434579547	10.614132257504119
TG(20:4_36:3)	9.866851352585655	9.874562356703537	11.148468557415754	9.881581328849622	10.105833092081753	9.876226830044473	11.285417329388654	10.556157979046587	NA	10.964672605345353	10.98085211218272	12.178667853990737	11.133486328028543	10.049131632512628	9.614357908	NA	9.809497345	10.404992800252684	10.62980578318175	11.154657632998289	10.41658691277766	11.037608608865455	10.657521617644845	10.59823098130875	11.413138282072875	10.219501713769063	NA	11.067423166664032	9.918303153258515
TG(22:6_36:2)	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
TG(22:6_38:1)	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
TG(22:6_38:2)	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	internal standard	Expected RT	precursor (m/z)	product (m/z)
TG(15:0/18:1(d7)/15:0)	NA	8.18	829.8	570.8
TG(18:0_36:2)	TG(15:0/18:1(d7)/15:0)	8.56	904.7	603.4
TG(18:1_34:2)	TG(15:0/18:1(d7)/15:0)	8.18	874.7	575.4
TG(18:1_34:3)	TG(15:0/18:1(d7)/15:0)	8	872.7	573.4
TG(20:4_32:1)	TG(15:0/18:1(d7)/15:0)	7.91	870.6	549.3
TG(20:4_34:2)	TG(15:0/18:1(d7)/15:0)	7.9	896.6	575.3
TG(20:4_34:3)	TG(15:0/18:1(d7)/15:0)	8.26	894.6	573.3
TG(20:4_36:0)	TG(15:0/18:1(d7)/15:0)	8.51	928.8	607.5
TG(20:4_36:2)	TG(15:0/18:1(d7)/15:0)	8.1	924.7	603.4
TG(20:4_36:3)	TG(15:0/18:1(d7)/15:0)	7.84	922.7	601.4
TG(22:6_36:2)	TG(15:0/18:1(d7)/15:0)	8.27	948.7	603.4
TG(22:6_38:1)	TG(15:0/18:1(d7)/15:0)	7.25	978.7	633.4
TG(22:6_38:2)	TG(15:0/18:1(d7)/15:0)	6.42	976.7	631.4
METABOLITES_END
#END