Summary of Study ST003501
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002147. The data can be accessed directly via it's Project DOI: 10.21228/M83F9Q This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003501 |
| Study Title | TREM2 expression level is critical for microglial state, metabolic capacity and efficacy of TREM2 agonism |
| Study Summary | Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator of microglial activity and sequence variants are major risk factors for late onset Alzheimer’s disease (LOAD). To better understand the molecular and functional changes associated with TREM2 signalling, we generated a TREM2 reporter mouse model and observed a gradual upregulation of reporter expression with increasing plaque proximity. Isolated microglia were sorted based on reporter expression and their transcriptomic profiles acquired in both wildtype and APP transgenic animals, allowing us to disentangle TREM2 versus pathology-specific effects. Bulk RNA sequencing highlighted TREM2 level-dependent changes in major immunometabolic pathways, with enrichment of genes in oxidative phosphorylation and cholesterol metabolism in microglia with increased TREM2 expression. To confirm these findings, we next analysed uptake of fluorodeoxyglucose (FDG) and examined metabolomic and lipidomic profiles. Again, independent of Aβ pathology, TREM2 expression correlated with uptake of FDG as well as increased cellular redox, energetics, and cholesterol homeostasis. Finally, we performed chronic treatment with a brain penetrant TREM2 agonist and identified a window of TREM2 expression where microglia are most responsive. Thus, our data provide novel insights into TREM2-mediated regulation of microglial metabolic function and informs current efforts to bring TREM2 agonists into clinical application. |
| Institute | Denali Therapeutics |
| Last Name | Suh |
| First Name | Jung |
| Address | 161 Oyster Point Blvd, South San Francisco, California, 94080, USA |
| suh@dnli.com | |
| Phone | +1 6507973837 |
| Submit Date | 2024-09-19 |
| Num Groups | 5 |
| Total Subjects | 26 |
| Num Males | 26 |
| Study Comments | Release as soon as it is possible |
| Publications | https://www.biorxiv.org/content/10.1101/2024.07.18.604115v1 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-09-30 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002147 |
| Project DOI: | doi: 10.21228/M83F9Q |
| Project Title: | TREM2 expression level is critical for microglial state, metabolic capacity and efficacy of TREM2 agonism |
| Project Type: | Preclinical Mouse study |
| Project Summary: | Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator of microglial activity and sequence variants are major risk factors for late onset Alzheimer’s disease (LOAD). To better understand the molecular and functional changes associated with TREM2 signalling, we generated a TREM2 reporter mouse model and observed a gradual upregulation of reporter expression with increasing plaque proximity. Isolated microglia were sorted based on reporter expression and their transcriptomic profiles acquired in both wildtype and APP transgenic animals, allowing us to disentangle TREM2 versus pathology-specific effects. Bulk RNA sequencing highlighted TREM2 level-dependent changes in major immunometabolic pathways, with enrichment of genes in oxidative phosphorylation and cholesterol metabolism in microglia with increased TREM2 expression. To confirm these findings, we next analysed uptake of fluorodeoxyglucose (FDG) and examined metabolomic and lipidomic profiles. Again, independent of Aβ pathology, TREM2 expression correlated with uptake of FDG as well as increased cellular redox, energetics, and cholesterol homeostasis. Finally, we performed chronic treatment with a brain penetrant TREM2 agonist and identified a window of TREM2 expression where microglia are most responsive. Thus, our data provide novel insights into TREM2-mediated regulation of microglial metabolic function and informs current efforts to bring TREM2 agonists into clinical application. |
| Institute: | Denali Therapeutics |
| Department: | Development Sciences |
| Last Name: | Suh |
| First Name: | Jung |
| Address: | 161 Oyster Point Blvd, South San Francisco, California, 94080, USA |
| Email: | suh@dnli.com |
| Phone: | +1 6507973837 |
| Funding Source: | Denali Therapeutics |
| Publications: | https://www.biorxiv.org/content/10.1101/2024.07.18.604115v1 |
Subject:
| Subject ID: | SU003630 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 15 mo |
| Gender: | Male |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | genotype | condition | group | Sample source |
|---|---|---|---|---|---|
| SA385741 | HSA-000019577 | APP | high | high_disease | microglia |
| SA385742 | HSA-000019588 | APP | high | high_disease | microglia |
| SA385743 | HSA-000019595 | APP | high | high_disease | microglia |
| SA385744 | HSA-000019574 | APP | high | high_disease | microglia |
| SA385745 | HSA-000019593 | APP | low | low_disease | microglia |
| SA385746 | HSA-000019575 | APP | low | low_disease | microglia |
| SA385747 | HSA-000019586 | APP | low | low_disease | microglia |
| SA385748 | HSA-000019572 | APP | low | low_disease | microglia |
| SA385749 | HSA-000019573 | APP | mid | mid_disease | microglia |
| SA385750 | HSA-000019594 | APP | mid | mid_disease | microglia |
| SA385751 | HSA-000019587 | APP | mid | mid_disease | microglia |
| SA385752 | HSA-000019576 | APP | mid | mid_disease | microglia |
| SA385753 | HSA-000019616 | NA | NA | NA | microglia |
| SA385754 | HSA-000019617 | NA | NA | NA | microglia |
| SA385755 | HSA-000019615 | NA | NA | NA | microglia |
| SA385756 | HSA-000019580 | WT | low | low_healthy | microglia |
| SA385757 | HSA-000019570 | WT | low | low_healthy | microglia |
| SA385758 | HSA-000019578 | WT | low | low_healthy | microglia |
| SA385759 | HSA-000019584 | WT | low | low_healthy | microglia |
| SA385760 | HSA-000019589 | WT | low | low_healthy | microglia |
| SA385761 | HSA-000019582 | WT | low | low_healthy | microglia |
| SA385762 | HSA-000019591 | WT | low | low_healthy | microglia |
| SA385763 | HSA-000019571 | WT | mid | mid_healthy | microglia |
| SA385764 | HSA-000019592 | WT | mid | mid_healthy | microglia |
| SA385765 | HSA-000019583 | WT | mid | mid_healthy | microglia |
| SA385766 | HSA-000019590 | WT | mid | mid_healthy | microglia |
| SA385767 | HSA-000019579 | WT | mid | mid_healthy | microglia |
| SA385768 | HSA-000019585 | WT | mid | mid_healthy | microglia |
| SA385769 | HSA-000019581 | WT | mid | mid_healthy | microglia |
| Showing results 1 to 29 of 29 |
Collection:
| Collection ID: | CO003623 |
| Collection Summary: | Microglia isolation was performed using the Magnetic-activated cell sorting (MACS) system (Miltenyi Biotec). No CD11b enrichment step was performed as the intrinsic mKate2 reporter is only expressed in TREM2 expressing (microglia) cells. Hence, fluorescence-activated cell sorting was performed based on the mKate2 fluorescence signal and sorted into low, mid and high expressing subpopulations, as a proxy for the TREM2 expression of individual cells. |
| Sample Type: | microglia |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003639 |
| Treatment Summary: | No treatment |
Sample Preparation:
| Sampleprep ID: | SP003637 |
| Sampleprep Summary: | Pellets from the sorted subpopulations were reconstituted on ice in 9:1 MeOH:water including internal standards, vortexed for 1 minute, and spun down for 5 minutes at 10,000 g. Supernatant was transferred to glass vial for analysis by LC-MS. |
Combined analysis:
| Analysis ID | AN005746 | AN005747 | AN005748 | AN005749 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC | Ion exchange |
| Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
| Column | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) | Imtakt Intrada Organic Acid (150 x 2mm, 3um) ) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex 6500+ Qtrap | ABI Sciex 6500+ Qtrap | ABI Sciex 6500+ Qtrap | ABI Sciex 6500+ Qtrap |
| Ion Mode | POSITIVE | POSITIVE | POSITIVE | NEGATIVE |
| Units | log2(area) | log2(area) | log2(area) | log2(area) |
Chromatography:
| Chromatography ID: | CH004361 |
| Chromatography Summary: | For each analysis, 5 µL of sample was injected on a BEH C18 1.7 µm, 2.1×100 mm column (Waters) using a flow rate of 0.25 mL/min at 55°C. For positive ionization mode, mobile phase A consisted of 60:40 acetonitrile/water (v/v) with 10 mM ammonium formate + 0.1% formic acid; mobile phase B consisted of 90:10 isopropyl alcohol/acetonitrile (v/v) with 10 mM ammonium formate + 0.1% formic acid. The gradient was programmed as follows: 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 9.1-10.0 min at 45% B. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 55 |
| 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 9.1-10.0 min at 45% B. |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 60% acetonitrile/40% water; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 90% isopropyl alcohol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004362 |
| Chromatography Summary: | For each analysis, 5 µL of sample was injected on a BEH amide 1.7 µm, 2.1×150 mm column (Waters Corporation, Milford, Massachusetts, USA) using a flow rate of 0.40 mL/min at 40°C. Mobile phase A consisted of water with 10 mM ammonium formate + 0.1% formic acid. Mobile phase B consisted of acetonitrile with 0.1% formic acid. The gradient was programmed as follows: 0.0–1.0 min at 95% B; 1.0–7.0 min to 50% B; 7.0–7.1 min to 95% B; and 7.1–10.0 min at 95% B. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0.0–1.0 min at 95% B; 1.0–7.0 min to 50% B; 7.0–7.1 min to 95% B; and 7.1–10.0 min at 95% B |
| Flow Rate: | 0.40 mL/min |
| Solvent A: | 100% water; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH004363 |
| Chromatography Summary: | 5 µL of sample was injected on an Imtakt Intrada Organic Acid 3 µm, 2 x 150 mm (Imtakt USA, Portland, OR USA); using a flow rate of 0.2 mL/min at 60°C. For negative ionization mode, Mobile phase A consisted of acetonitrile/water/formic acid = 10/90/0.1%. Mobile phase B consisted of acetonitrile/ 100mM ammonium formate= 10/90%. The gradient was programmed as follows: 0.0–1.0 min at 0% B; 1.0–7.0 min to 100% B; 7.1 at 0% B; and 7.1-10 min at 0% B. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Imtakt Intrada Organic Acid (150 x 2mm, 3um) ) |
| Column Temperature: | 60 |
| Flow Gradient: | 0.0–1.0 min at 0% B; 1.0–7.0 min to 100% B; 7.1 at 0% B; and 7.1-10 min at 0% B. |
| Flow Rate: | 0.20 mL/min |
| Solvent A: | 10% acetonitrile/90% water; 0.1% formic acid |
| Solvent B: | 10% acetonitrile/90% water; 100mM ammonium formate |
| Chromatography Type: | Ion exchange |
MS:
| MS ID: | MS005469 |
| Analysis ID: | AN005746 |
| Instrument Name: | ABI Sciex 6500+ Qtrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Curtain gas at 40 psi (positive mode); collision gas was set at medium; ion spray voltage at 5500 V (positive mode); temperature at 250°C (positive mode); ion source Gas 1 at 55 psi; ion source Gas 2 at 60 psi; entrance potential at 10 V (positive mode); and collision cell exit potential at 12.5 V (positive mode). Quantification was performed using MultiQuant 3.02 (Sciex). |
| Ion Mode: | POSITIVE |
| MS ID: | MS005470 |
| Analysis ID: | AN005747 |
| Instrument Name: | ABI Sciex 6500+ Qtrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Curtain gas at 40 psi (positive mode); collision gas was set at medium; ion spray voltage at 5500 V (positive mode); temperature at 250°C (positive mode); ion source Gas 1 at 55 psi; ion source Gas 2 at 60 psi; entrance potential at 10 V (positive mode); and collision cell exit potential at 12.5 V (positive mode). Quantification was performed using MultiQuant 3.02 (Sciex). Increased MRM dwell time for specific list of TG transitions. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005471 |
| Analysis ID: | AN005748 |
| Instrument Name: | ABI Sciex 6500+ Qtrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | curtain gas at 30 psi; collision gas was set at medium; ion spray voltage at 5500 V; temperature at 600°C; ion source Gas 1 at 50 psi; ion source Gas 2 at 60 psi; entrance potential at 10 V; and collision cell exit potential at 12.5 V. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005472 |
| Analysis ID: | AN005749 |
| Instrument Name: | ABI Sciex 6500+ Qtrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | curtain gas at 40 V; collision gas was set at medium; ion spray voltage at -4500 V; temperature at 600°C; ion source Gas 1 at 50 psi; ion source Gas 2 at 60 psi; entrance potential at -10 V; and collision cell exit potential at -15.0 V. |
| Ion Mode: | NEGATIVE |
