Summary of Study ST004059
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 PR002548. The data can be accessed directly via it's Project DOI: 10.21228/M8926N 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 | ST004059 |
| Study Title | Targeted Lipid and Metabolite Profiling in Brains of ATP13A2 Knockout Mice |
| Study Summary | Comprehensive targeted profiling of lipids and metabolites was conducted in brain tissues from ATP13A2 knockout mice at 4.5 and 15 months of age to assess ATP13A2 deletion and its association with lysosomal dysfunction. |
| 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 06507973837 |
| Submit Date | 2025-07-07 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-07-23 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002548 |
| Project DOI: | doi: 10.21228/M8926N |
| Project Title: | Lysosomal polyamine storage upon ATP13A2 loss impairs β-glucocerebrosidase via altered lysosomal pH and electrostatic hydrolase-lipid interactions |
| Project Type: | Preclinical Mouse and cellular studies |
| Project Summary: | ATP13A2 is an endolysosomal polyamine transporter mutated in several neurodegenerative conditions involving lysosomal defects, including Parkinson’s disease (PD). While polyamines are polybasic and polycationic molecules that play pleiotropic cellular roles, their specific impact on lysosomal health is unknown. Here, we demonstrate lysosomal polyamine accumulation in ATP13A2 knockout (KO) cell lines. Primary polyamine storage caused secondary storage of lysosomal anionic phospholipid bis(monoacylglycero)phosphate (BMP) and age-dependent increase in the β-glucocerebrosidase (GCase) substrate, glucosylsphingosine, in Atp13a2 KO brains. Polyamine accumulation inhibited lysosomal GCase activity in cells and this was reversed by lysosome reacidification or BMP supplementation. A liposome-based GCase assay utilizing physiological substrates demonstrated dose-dependent inhibition of BMP-stimulated GCase activity by polyamines, in part via a pH-independent, electrostatics-based mechanism. Therefore, excess polyamine compromises lysosomes by disrupting pH and electrostatic interactions between GCase and BMP enabling efficient substrate hydrolysis, potentially clarifying their pathogenic mechanisms, and suggesting convergence on PD-relevant pathways. |
| Institute: | Denali Therapeutics |
| Last Name: | Suh |
| First Name: | Jung |
| Address: | 161 Oyster Point Blvd, South San Francisco, California, 94080, USA |
| Email: | suh@dnli.com |
| Phone: | +1 6507973837 |
Subject:
| Subject ID: | SU004205 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | genotype | Sample source |
|---|---|---|---|
| SA469385 | HSA-000034472 | HET KO ATP13A2 | brain |
| SA469386 | HSA-000034496 | HET KO ATP13A2 | brain |
| SA469387 | HSA-000034493 | HET KO ATP13A2 | brain |
| SA469388 | HSA-000034499 | HET KO ATP13A2 | brain |
| SA469389 | HSA-000034487 | HET KO ATP13A2 | brain |
| SA469390 | HSA-000034490 | HET KO ATP13A2 | brain |
| SA469391 | HSA-000034502 | HET KO ATP13A2 | brain |
| SA469392 | HSA-000034469 | HET KO ATP13A2 | brain |
| SA469393 | HSA-000034475 | HET KO ATP13A2 | brain |
| SA469394 | HSA-000034466 | HET KO ATP13A2 | brain |
| SA469395 | HSA-000034481 | HET KO ATP13A2 | brain |
| SA469396 | HSA-000034478 | HET KO ATP13A2 | brain |
| SA469397 | HSA-000034489 | HOM KO ATP13A2 | brain |
| SA469398 | HSA-000034468 | HOM KO ATP13A2 | brain |
| SA469399 | HSA-000034504 | HOM KO ATP13A2 | brain |
| SA469400 | HSA-000039091 | HOM KO ATP13A2 | brain |
| SA469401 | HSA-000034474 | HOM KO ATP13A2 | brain |
| SA469402 | HSA-000034480 | HOM KO ATP13A2 | brain |
| SA469403 | HSA-000034477 | HOM KO ATP13A2 | brain |
| SA469404 | HSA-000034486 | HOM KO ATP13A2 | brain |
| SA469405 | HSA-000034471 | HOM KO ATP13A2 | brain |
| SA469406 | HSA-000038799 | HOM KO ATP13A2 | brain |
| SA469407 | HSA-000038787 | HOM KO ATP13A2 | brain |
| SA469408 | HSA-000034483 | HOM KO ATP13A2 | brain |
| SA469409 | HSA-000034492 | HOM KO ATP13A2 | brain |
| SA469410 | HSA-000038797 | HOM KO ATP13A2 | brain |
| SA469411 | HSA-000034498 | HOM KO ATP13A2 | brain |
| SA469412 | HSA-000034495 | HOM KO ATP13A2 | brain |
| SA469413 | HSA-000034465 | HOM KO ATP13A2 | brain |
| SA469414 | HSA-000038803 | HOM KO ATP13A2 | brain |
| SA469415 | HSA-000038811 | HOM KO ATP13A2 | brain |
| SA469416 | HSA-000038810 | HOM KO ATP13A2 | brain |
| SA469417 | HSA-000038801 | HOM KO ATP13A2 | brain |
| SA469418 | HSA-000038812 | HOM KO ATP13A2 | brain |
| SA469419 | HSA-000038809 | HOM KO ATP13A2 | brain |
| SA469420 | HSA-000038790 | HOM KO ATP13A2 | brain |
| SA469421 | HSA-000034501 | HOM KO ATP13A2 | brain |
| SA469422 | HSA-000038794 | HOM KO ATP13A2 | brain |
| SA469423 | HSA-000039092 | NA | brain |
| SA469424 | HSA-000035026 | NA | brain |
| SA469425 | HSA-000035025 | NA | brain |
| SA469426 | HSA-000038789 | NA | brain |
| SA469427 | HSA-000038808 | NA | brain |
| SA469428 | HSA-000035023 | NA | brain |
| SA469429 | HSA-000039094 | NA | brain |
| SA469430 | HSA-000038795 | NA | brain |
| SA469431 | HSA-000038807 | NA | brain |
| SA469432 | HSA-000034505 | NA | brain |
| SA469433 | HSA-000035024 | NA | brain |
| SA469434 | HSA-000034484 | NA | brain |
| SA469435 | HSA-000038793 | WT | brain |
| SA469436 | HSA-000034485 | WT | brain |
| SA469437 | HSA-000034497 | WT | brain |
| SA469438 | HSA-000034503 | WT | brain |
| SA469439 | HSA-000038788 | WT | brain |
| SA469440 | HSA-000034488 | WT | brain |
| SA469441 | HSA-000034491 | WT | brain |
| SA469442 | HSA-000034494 | WT | brain |
| SA469443 | HSA-000038796 | WT | brain |
| SA469444 | HSA-000034500 | WT | brain |
| SA469445 | HSA-000038792 | WT | brain |
| SA469446 | HSA-000038814 | WT | brain |
| SA469447 | HSA-000038813 | WT | brain |
| SA469448 | HSA-000038804 | WT | brain |
| SA469449 | HSA-000038805 | WT | brain |
| SA469450 | HSA-000038802 | WT | brain |
| SA469451 | HSA-000039093 | WT | brain |
| SA469452 | HSA-000038806 | WT | brain |
| SA469453 | HSA-000034470 | WT | brain |
| SA469454 | HSA-000038798 | WT | brain |
| SA469455 | HSA-000034479 | WT | brain |
| SA469456 | HSA-000034467 | WT | brain |
| SA469457 | HSA-000038791 | WT | brain |
| SA469458 | HSA-000034464 | WT | brain |
| SA469459 | HSA-000034476 | WT | brain |
| SA469460 | HSA-000034482 | WT | brain |
| SA469461 | HSA-000034473 | WT | brain |
| SA469462 | HSA-000038800 | WT | brain |
| Showing results 1 to 78 of 78 |
Collection:
| Collection ID: | CO004198 |
| Collection Summary: | Heterozygous Atp13a2<tm1Pjsch> animals of genotype B6N.129S6(Cg)-Atp13a2tm1Pjsch/J were obtained from The Jackson Laboratory (JAX strain 021914)17 and were crossed to generate homozygous Atp13a2 KO (Atp13a2 –/–) animals. For both the 5-month and 15-month-old cohort, female and male mice were used in comparable percentages (see table below). In case of the 15-month-old Atp13a2 KO cohort, one of the animals died prior to study conclusion and was excluded. Animals were maintained and all procedures performed in adherence to ethical regulations and protocols approved by the Denali Therapeutics Inc. Institutional Animal Care and Use Committee (IACUC). Mice were housed under a 12-h light/12-h dark cycle and had access to water and standard rodent diet ad libitum. Running wheels were provided for enrichment to the cohort that was aged to 15 months.Animals were deeply anesthetized via intraperitoneal injection of 2.5% Avertin and transcardially perfused with ice-cold PBS using a peristaltic pump (Gilson Inc. Minipuls Evolution). The brain was then removed and one hemisphere sub-dissected into the anterior cortex and hippocampus, while the other was retained without sub-dissection. Tissue samples were individually weighed, flash frozen on dry ice and stored at -80°C for subsequent analysis. |
| Sample Type: | Brain |
| Storage Conditions: | -80℃ |
| Collection Vials: | Lobind 1.5 mL Eppendorf tubes |
| Storage Vials: | Lobind 1.5 mL Eppendorf tubes |
Treatment:
| Treatment ID: | TR004214 |
| Treatment Summary: | No treatment |
Sample Preparation:
| Sampleprep ID: | SP004211 |
| Sampleprep Summary: | For tissue samples, 20 (± 3) mg of anterior cortex or 15 (± 2) mg of hippocampus from the left hemisphere of each individual animal was dissected, weighed and flash frozen during tissue collection. Lipids and metabolites were extracted from the frozen samples using 400 mL of HPLC-grade methanol (Fisher Chemical; # A452-4) containing stable-isotope internal standards and homogenized with a 3 mm tungsten carbide bead for 45 s at 25 Hz on TissueLyzer II (QIAGEN, #85300). The methanol fraction was isolated via centrifugation (20 min at 4°C, 14,000 x g, transferred to a 96-well sample collection plate (Waters; #186005837) and incubated for 1 h, at -20°C for protein precipitation, followed by an additional 20 min centrifugation (4,000 x g at 4°C). The supernatant was transferred to glass vial plates (Analytical systems, #27350) for LCMS analysis. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -20℃ |
Chromatography:
| Chromatography ID: | CH005100 |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Imtakt Intrada Organic Acid (150 × 2 mm, 3 um) |
| Column Temperature: | 55 |
| 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 |
| Chromatography ID: | CH005101 |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 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: | HILIC |
| Chromatography ID: | CH005102 |
| 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: | CH005103 |
| 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 acetate; 0.1% acetic acid |
| Solvent B: | 90% isopropyl alcohol/10% acetonitrile; 10 mM ammonium acetate; 0.1% acetic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005104 |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent 300 SB-C18 RRHD (100 x 2.1 mm, 1.8um) |
| Column Temperature: | 20 |
| Flow Gradient: | 0.00–0.25 min at 0% B, 0.25–4.00 min from 0% B to 50% B, 4.00–4.50 min from 50% B to 100% B, 4.50–5.10 min at 100% B, 5.10–5.11 min to 0% B, and 5.11–5.79 min at 0% B |
| Flow Rate: | 0.80 mL/min |
| Solvent A: | 100% water; 0.2% formic acid |
| Solvent B: | 100% acetonitrile; 0.2% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005105 |
| Chromatography Summary: | Advanced Materials Technology HALO HILIC column (150 x 3.0 mm, 2um); #91813 |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Advanced Materials Technology HALO HILIC (150 x 3.0 mm, 2um) |
| Column Temperature: | 45 |
| Flow Gradient: | 0.0–2.0 min, 100% B; 2.1 min, 95% B; 4.5 min, 85% B; held at 85% B until 6.0 min; 6.1 min, 0% B; held at 0% B until 8.5 min |
| Flow Rate: | 0.45 mL/min |
| Solvent A: | 92.5% acetonitrile/5% isopropanol/2.5% water; 5 mM ammonium formate; 0.5% formic acid |
| Solvent B: | 92.5% water/5% isopropanol/2.5% acetonitrile; 5 mM ammonium formate; 0.5% formic acid |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN006712 |
| Analysis Type: | MS |
| Chromatography ID: | CH005100 |
| Num Factors: | 4 |
| Num Metabolites: | 59 |
| Units: | normalized peak area |
| Analysis ID: | AN006713 |
| Analysis Type: | MS |
| Chromatography ID: | CH005101 |
| Num Factors: | 4 |
| Num Metabolites: | 216 |
| Units: | normalized peak area |
| Analysis ID: | AN006714 |
| Analysis Type: | MS |
| Chromatography ID: | CH005102 |
| Num Factors: | 4 |
| Num Metabolites: | 140 |
| Units: | normalized peak area |
| Analysis ID: | AN006715 |
| Analysis Type: | MS |
| Chromatography ID: | CH005103 |
| Num Factors: | 4 |
| Num Metabolites: | 119 |
| Units: | normalized peak area |
| Analysis ID: | AN006716 |
| Analysis Type: | MS |
| Chromatography ID: | CH005103 |
| Num Factors: | 4 |
| Num Metabolites: | 15 |
| Units: | normalized peak area |
| Analysis ID: | AN006717 |
| Analysis Type: | MS |
| Chromatography ID: | CH005104 |
| Num Factors: | 4 |
| Num Metabolites: | 58 |
| Units: | normalized peak area |
| Analysis ID: | AN006718 |
| Analysis Type: | MS |
| Chromatography ID: | CH005105 |
| Num Factors: | 4 |
| Num Metabolites: | 39 |
| Units: | normalized peak area |
