Summary of Study ST002268
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 PR001450. The data can be accessed directly via it's Project DOI: 10.21228/M89703 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 | ST002268 |
| Study Title | Autophagy-related protein PIK3C3 maintains healthy brown and white adipose tissues to prevent metabolic diseases |
| Study Type | Lipidomics |
| Study Summary | Adequate mass and function of adipose tissues (ATs) play an essential role in preventing metabolic perturbations. Pathological reduction of ATs in lipodystrophy leads to an array of metabolic diseases. Understanding the underlying mechanisms may benefit the development of effective therapies. Several cellular processes, including autophagy, function collectively to maintain AT homeostasis. Here, we investigated the impact of adipocyte-specific deletion of the autophagy-related lipid kinase PIK3C3 on AT homeostasis and systemic metabolism in mice. We report that PIK3C3 functions in all ATs and that its absence disturbs adipocyte autophagy and hinders adipocyte differentiation, survival, and function with differential effects on brown and white ATs. These abnormalities caused loss of white ATs, whitening followed by loss of brown ATs, and impaired browning of white ATs. Consequently, mice exhibited compromised thermogenic capacity and developed dyslipidemia, hepatic steatosis, insulin resistance and type 2 diabetes. While these effects of PIK3C3 contrast previous findings with the autophagy-related protein ATG7 in adipocytes, mice with a combined deficiency in both factors revealed a dominant role of the PIK3C3-deficient phenotype. We also found that dietary lipid excess exacerbates AT pathologies caused by PIK3C3 deficiency. Surprisingly, glucose tolerance was spared in adipocyte-specific PIK3C3-deficient mice, a phenotype that was more evident during dietary lipid excess. These findings reveal a crucial yet complex role for PIK3C3 in ATs and suggest the potential of targeting this factor for therapeutic intervention in metabolic diseases. |
| Institute | Vanderbilt University |
| Department | Chemistry |
| Laboratory | Center for Innovative Technology |
| Last Name | Leaptrot |
| First Name | Katrina |
| Address | 1234 Stevenson Center Ln |
| katrina.l.leaptrot@vanderbilt.edu | |
| Phone | 6158758422 |
| Submit Date | 2022-08-26 |
| Num Groups | 4 |
| Total Subjects | 16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-02-26 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001450 |
| Project DOI: | doi: 10.21228/M89703 |
| Project Title: | Autophagy-related protein PIK3C3 maintains healthy brown and white adipose tissues to prevent metabolic diseases |
| Project Type: | Lipidomics |
| Project Summary: | Adequate mass and function of adipose tissues (ATs) play an essential role in preventing metabolic perturbations. Pathological reduction of ATs in lipodystrophy leads to an array of metabolic diseases. Understanding the underlying mechanisms may benefit the development of effective therapies. Several cellular processes, including autophagy, function collectively to maintain AT homeostasis. Here, we investigated the impact of adipocyte-specific deletion of the autophagy-related lipid kinase PIK3C3 on AT homeostasis and systemic metabolism in mice. We report that PIK3C3 functions in all ATs and that its absence disturbs adipocyte autophagy and hinders adipocyte differentiation, survival, and function with differential effects on brown and white ATs. These abnormalities caused loss of white ATs, whitening followed by loss of brown ATs, and impaired browning of white ATs. Consequently, mice exhibited compromised thermogenic capacity and developed dyslipidemia, hepatic steatosis, insulin resistance and type 2 diabetes. While these effects of PIK3C3 contrast previous findings with the autophagy-related protein ATG7 in adipocytes, mice with a combined deficiency in both factors revealed a dominant role of the PIK3C3-deficient phenotype. We also found that dietary lipid excess exacerbates AT pathologies caused by PIK3C3 deficiency. Surprisingly, glucose tolerance was spared in adipocyte-specific PIK3C3-deficient mice, a phenotype that was more evident during dietary lipid excess. These findings reveal a crucial yet complex role for PIK3C3 in ATs and suggest the potential of targeting this factor for therapeutic intervention in metabolic diseases. |
| Institute: | Vanderbilt University |
| Department: | Chemistry |
| Laboratory: | Center for Innovative Technology |
| Last Name: | Leaptrot |
| First Name: | Katrina |
| Address: | 1234 Stevenson Center Ln |
| Email: | katrina.l.leaptrot@vanderbilt.edu |
| Phone: | 6158758422 |
Subject:
| Subject ID: | SU002354 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | Pik3c3f/f mice |
| Age Or Age Range: | W24 |
| Gender: | Male and female |
| Animal Animal Supplier: | Jackson Laboratory |
| Animal Housing: | pathogen-free conditions at a controlled room temperature |
| Animal Light Cycle: | 12-hour light/dark cycle |
| Animal Feed: | regular chow diet (5LOD, LabDiet) |
| Animal Water: | ad lib |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Lipid Type |
|---|---|---|---|
| SA217546 | BAT-KO-S6 | KO | Brown adipose tissue |
| SA217547 | BAT-KO-S8 | KO | Brown adipose tissue |
| SA217548 | BAT-KO-S5 | KO | Brown adipose tissue |
| SA217549 | BAT-KO-S7 | KO | Brown adipose tissue |
| SA217550 | VAT-KO-S15 | KO | White adipose tissue |
| SA217551 | VAT-KO-S13 | KO | White adipose tissue |
| SA217552 | VAT-KO-S14 | KO | White adipose tissue |
| SA217553 | VAT-KO-S16 | KO | White adipose tissue |
| SA217554 | BAT-WT-S1 | WT | Brown adipose tissue |
| SA217555 | BAT-WT-S3 | WT | Brown adipose tissue |
| SA217556 | BAT-WT-S4 | WT | Brown adipose tissue |
| SA217557 | BAT-WT-S2 | WT | Brown adipose tissue |
| SA217558 | VAT-WT-S9 | WT | White adipose tissue |
| SA217559 | VAT-WT-S10 | WT | White adipose tissue |
| SA217560 | VAT-WT-S11 | WT | White adipose tissue |
| SA217561 | VAT-WT-S12 | WT | White adipose tissue |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO002347 |
| Collection Summary: | Mice were housed under specific pathogen-free conditions, fed with a regular chow diet (5LOD, LabDiet), provided food and water ad lib unless otherwise specified, and maintained on a 12-hour light/dark cycle at a controlled room temperature of 22°C, except for the cold treatment studies. Mice were sacrificed at non-fasting state for further analysis unless otherwise specified. |
| Collection Protocol Filename: | Materials_and_Methods.pdf |
| Sample Type: | Adipose tissue |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002366 |
| Treatment Summary: | We generated Adipoq-Cre;Pik3c3f/f (cKO) and Pik3c3f/f (WT) mice and analyzed interscapular BAT (iBAT), inguinal subcutaneous WAT (iWAT), and perigonadal visceral WAT (pWAT). |
Sample Preparation:
| Sampleprep ID: | SP002360 |
| Sampleprep Summary: | The iBAT and pWAT was harvestedat sacrifice from mice at W24. Samples were immediately frozen in liquid nitrogen followed by -80°C storage before analysis. Both WT (n=4) and cKO (n=4) mice were analyzed. Adipose tissue samples, ranging from 10-30 mg, were thawed on ice and mixed with 1 mL of cold 1:1:2 (v:v:v) methanol MeOH:ACN:H2O with 50 mM ammonium bicarbonate lysis buffer. Samples were homogenized using a tissue homogenizer operated at 20,000 rpm for 10 seconds to break the tissue, then vortex mixed for 10 seconds. An appropriate volume of lysate was transferred from each sample such that individual samples were normalized based on tissue amount. Following volume adjustment to 200 L, 800 L of cold MeOH was added to the samples. Individual samples were vortexed for 30 seconds and incubated overnight at -80°C for protein precipitation. Following incubation, samples were centrifuged for 15 min at 15,000 rpm at 4°C and the supernatant was transferred to a new labeled tube and dried down using a cold vacuum centrifuge. Samples were reconstituted in 100 L H2O, 100 L MeOH, and 10 μL of SPLASH LIPIDOMIX with vortex mixing after each addition. Samples were incubated at room temperature for 10 min followed |
| Sampleprep Protocol Filename: | Global untargeted lipidomics.pdf |
Combined analysis:
| Analysis ID | AN003705 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 |
| Column | Thermo Hypersil Gold (100 x 2.mm,1.9um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6560 Ion Mobility |
| Ion Mode | POSITIVE |
| Units | retention time underscore m/z |
Chromatography:
| Chromatography ID: | CH002744 |
| Methods Filename: | Global_untargeted_lipidomics.pdf |
| Instrument Name: | Agilent 1290 |
| Column Name: | Thermo Hypersil Gold (100 x 2.mm,1.9um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003454 |
| Analysis ID: | AN003705 |
| Instrument Name: | Agilent 6560 Ion Mobility |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Data analysis was performed using Progenesis QI software (version 3.0, Nonlinear Dynamics, Newcastle, UK). Retention time alignment, peak picking, and peak deconvolution used default parameters. Spectra were normalized to all compounds, and data were filtered for coefficients of variance < 25% in QC technical replicate injections. A prioritized compound list was generated via a one-factor ANOVA, with four experimental groups for comparison including wild type and Vps34 knockout for both brown and visceral adipose tissue. Lipids were considered to be differentially altered if the p-value < 0.05 and the fold change was greater than Ι2Ι. Significantly changed compounds were selected for annotation. Lipidomic annotations were performed using a previously described classification system with compounds being assigned a confidence level of 1 to 5 (1 being the highest confidence) with improved confidence requiring more supporting evidence such as accurate mass, MS/MS fragmentation, and retention time matching to standards. Lipid annotated were performed with reference to in-house and online databases (MS-DIAL, LipidMatch, and Lipid Annotator). Differentially abundant lipids (DALs) were uploaded into the LIPEA algorithm for pathway enrichment analysis. Corrected p-values were calculated using Benjamini correction and a p-value <0.05 was used to determine significantly affected pathways. |
| Ion Mode: | POSITIVE |
