Summary of Study ST002938
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 PR001828. The data can be accessed directly via it's Project DOI: 10.21228/M8F14S 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 | ST002938 |
| Study Title | Role of PI3K in Atrial Myopathy: Insights from Transgenic Mouse Models and Identification of a Dysregulated PI3K Lipid Profile in Individuals with Atrial Fibrillation - part 1 of 2, human plasma |
| Study Summary | Here, we assessed whether there was any evidence of dysregulation in IGF1R-PI3K signaling in veteran male athletes with/without AF by assessing their plasma lipid species. This was following evidence of dysregulation of the PI3K signaling cascade in the atria of mice that had undergone extreme exercise training, together with pathology in dnPI3K Tg(+/+) mice. |
| Institute | Baker Heart and Diabetes Institute |
| Laboratory | Metabolomics |
| Last Name | Tham |
| First Name | Yow |
| Address | 75 Commercial Rd, Melbourne, Victoria, 3004, Australia |
| yowkeat.tham@baker.edu.au | |
| Phone | 0430502623 |
| Submit Date | 2023-10-11 |
| Num Groups | 2 |
| Total Subjects | 78 |
| Num Males | 78 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-01-12 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001828 |
| Project DOI: | doi: 10.21228/M8F14S |
| Project Title: | Role of PI3K in Atrial Myopathy: Insights from Transgenic Mouse Models and Identification of a Dysregulated PI3K Lipid Profile in Individuals with Atrial Fibrillation |
| Project Summary: | In a serendipitous discovery, atrial enlargement, fibrosis and thrombi was identified in a subset of transgenic mice with reduced phosphoinositide 3-kinase (PI3K, class IA) in cardiac myocytes. Understanding mechanisms underlying atrial myopathy has important implications for understanding and preventing atrial fibrillation (AF). Prior work had shown that PI3K is an essential regulator of exercise-induced ventricular enlargement and protection, but the role in the atria was unknown. Further, while targeting IGF1-PI3K-Akt signaling has been considered a potential therapeutic strategy for the failing heart, growing evidence suggests fine-tuning IGF1-PI3K signaling would be necessary. Here, we undertook comprehensive physiological and molecular analyses in cardiac-specific transgenic mice with increased or decreased PI3K to assess the dose response impact of directly regulating PI3K. Elevated PI3K was associated with a dose-dependent increase in heart size, and preserved/enhanced function. In contrast, reduced PI3K led to cardiac dysfunction, fibrosis, arrhythmia, and increased susceptibility to atrial enlargement and thrombi. This phenotype was associated with dysregulation of a lipid species (GM3) that regulates the IGF1-PI3K pathway, cardiac stress and contractility genes. Proteomic profiling identified distinct signatures across atria with varying degrees of atrial dysfunction, enlargement, and presence of atrial thrombi. To assess the potential relevance in humans we assessed circulating PI3K-related lipids in plasma from athletes with/without AF. Dysregulation of GM3 and PI3K-related lipids were identified in athletes with AF. Collectively, this work advances our understanding of mechanisms underpinning atrial pathophysiology, offers new insights for therapeutic approaches targeting atrial myopathy and AF, and has identified potential new lipid markers for identifying individuals at risk of AF. |
| Institute: | Baker Heart and Diabetes Institute |
| Laboratory: | Metabolomics |
| Last Name: | Tham |
| First Name: | Yow Keat |
| Address: | 75 Commercial Rd, Melbourne, Victoria, 3004, Australia |
| Email: | yowkeat.tham@baker.edu.au |
| Phone: | 0430502623 |
Subject:
| Subject ID: | SU003051 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | >40 |
| Gender: | Male |
| Human Inclusion Criteria: | The athletes (>40 years) had all been engaged in endurance sports training and competition for more than 10 years (e.g. rowing, triathlon, cycling and cross-country skiing) |
| Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Grouping |
|---|---|---|
| SA319395 | PAFH25_SE | Athlete AF |
| SA319396 | PAFH34_LE | Athlete AF |
| SA319397 | PAFH33_PD | Athlete AF |
| SA319398 | PAFH27_AS | Athlete AF |
| SA319399 | PAFHR29_HM | Athlete AF |
| SA319400 | PAFHR31_DY | Athlete AF |
| SA319401 | PAFHR30_MV | Athlete AF |
| SA319402 | PAFH32_MS | Athlete AF |
| SA319403 | PAFH13_CP | Athlete AF |
| SA319404 | PAFH28_CB | Athlete AF |
| SA319405 | PAFH17_JA | Athlete AF |
| SA319406 | PAFH16_PP | Athlete AF |
| SA319407 | PAFH15_GT | Athlete AF |
| SA319408 | PAFH18_DC | Athlete AF |
| SA319409 | PAFH19_RB | Athlete AF |
| SA319410 | PAFHR44_JJ | Athlete AF |
| SA319411 | PAFH22_HH | Athlete AF |
| SA319412 | PAFH36_NP | Athlete AF |
| SA319413 | PAFH30_PW | Athlete AF |
| SA319414 | PAFHR51_DF | Athlete AF |
| SA319415 | PAFHR20_RY | Athlete AF |
| SA319416 | PAFHR14_JW | Athlete AF |
| SA319417 | PAFHR11_SS | Athlete AF |
| SA319418 | PAFHR21_GJ | Athlete AF |
| SA319419 | PAFHR24_JS | Athlete AF |
| SA319420 | PAFHR36_PH | Athlete AF |
| SA319421 | PAFHR5_PM | Athlete AF |
| SA319422 | PAFHR25_PN | Athlete AF |
| SA319423 | PAFHR3_JN | Athlete AF |
| SA319424 | PAFHR2_AC | Athlete AF |
| SA319425 | PAFHR56_WB | Athlete AF |
| SA319426 | PAFHR53_GB | Athlete AF |
| SA319427 | PAFHR52_AJ | Athlete AF |
| SA319428 | PAFHR57_JT | Athlete AF |
| SA319429 | PAFHR64_WG | Athlete AF |
| SA319430 | PAFHR1_EM | Athlete AF |
| SA319431 | PAFHR78_LB | Athlete AF |
| SA319432 | PAFH14_GVDP | Athlete AF |
| SA319433 | PAFH21_JT | Athlete AF |
| SA319434 | PAFH9_DB | Athlete AF |
| SA319435 | PAFH6_SS | Athlete AF |
| SA319436 | PAFHR27_SJ | Athlete Non-AF |
| SA319437 | PAFHR58_MB | Athlete Non-AF |
| SA319438 | PAFHR8_JH | Athlete Non-AF |
| SA319439 | PAFHR60_PN | Athlete Non-AF |
| SA319440 | PAFHR34_LP | Athlete Non-AF |
| SA319441 | PAFHR76_NG | Athlete Non-AF |
| SA319442 | PAFHR42_CR | Athlete Non-AF |
| SA319443 | PAFHR40_GX | Athlete Non-AF |
| SA319444 | PAFHR46_MS | Athlete Non-AF |
| SA319445 | PAFHR68_GP | Athlete Non-AF |
| SA319446 | PAFHR12_AM | Athlete Non-AF |
| SA319447 | PAFHR17_JS | Athlete Non-AF |
| SA319448 | PAFHR41_AM | Athlete Non-AF |
| SA319449 | PAFHR23_PA | Athlete Non-AF |
| SA319450 | PAFHR33_RG | Athlete Non-AF |
| SA319451 | PAFHR75_AP | Athlete Non-AF |
| SA319452 | PAFHR9_IF | Athlete Non-AF |
| SA319453 | PAFHR77_ID | Athlete Non-AF |
| SA319454 | PAFHR19_PB | Athlete Non-AF |
| SA319455 | PAFHR79_RA | Athlete Non-AF |
| SA319456 | PAFHR72_AM | Athlete Non-AF |
| SA319457 | PAFHR48_AI | Athlete Non-AF |
| SA319458 | PAFHR47_PVV | Athlete Non-AF |
| SA319459 | PAFHR37_JM | Athlete Non-AF |
| SA319460 | PAFHR28_SY | Athlete Non-AF |
| SA319461 | PAFHR18_BL | Athlete Non-AF |
| SA319462 | PAFHX12_DA | Athlete Non-AF |
| SA319463 | PAFHR38_JL | Athlete Non-AF |
| SA319464 | PAFHR6_GL | Athlete Non-AF |
| SA319465 | PAFHR49_MP | Athlete Non-AF |
| SA319466 | PAFHR39_CS | Athlete Non-AF |
| SA319467 | PAFHR61_PS | Athlete Non-AF |
| SA319468 | PAFHR50_RW | Athlete Non-AF |
| SA319469 | PAFHR15_TY | Athlete Non-AF |
| SA319470 | PAFHR16_FR | Athlete Non-AF |
| SA319471 | PAFHR54_HF | Athlete Non-AF |
| SA319472 | PAFHR4_WM | Athlete Non-AF |
| Showing results 1 to 78 of 78 |
Collection:
| Collection ID: | CO003044 |
| Collection Summary: | Blood was collected from participants after fasting (no eating or drinking 8-12hours prior) Blood was stored in EDTA blood tubes and placed on ice. Tubes were then spun at 3000 rpm for 10 minutes at 4 degrees. Plasma is then collected as supernatant from the tube and aliquoted into fresh tubes. |
| Sample Type: | Blood (plasma) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003060 |
| Treatment Summary: | no treatment was done |
Sample Preparation:
| Sampleprep ID: | SP003057 |
| Sampleprep Summary: | Lipid extraction was conducted using 10ul of plasma using the single phase chloroform methanol method. 10ul of internal standards and 200ul of chloroform:methanol (1:2) were added to samples before the mixture was vortexed. Samples were then placed on a rotary shaker for 10 mins at a speed of 90 before being transferred to a bath sonicator. Samples were then sonicated for 30 mins at water temperature below 28 degrees. Samples were then removed and rested at room temperature for 20 mins. Samples were then centrifuged at 13000rpm for 10 minutes. 200ul of the supernatant was then transferred to 0.5ml polypropylene 96 well plates, and spun dried using a speedvac vacuum concentrator. Lipids were reconstituted in 50ul water saturated butanol + 50ul of Ammonium Formate. |
| Sampleprep Protocol Filename: | Agilent_appnote.pdf |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN004823 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 Infinity II |
| Column | Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6490 QQQ |
| Ion Mode | POSITIVE |
| Units | pmol/ml |
Chromatography:
| Chromatography ID: | CH003643 |
| Chromatography Summary: | The running solvent consisted of solvent A: 50% H2O / 30% acetonitrile / 20% isopropanol (v/v/v) containing 10mM ammonium formate and 5uM medronic acid, and solvent B: 1% H2O / 9% acetonitrile / 90% isopropanol (v/v/v) containing 10mM ammonium formate. We utilized a stepped linear gradient with a 16-minute cycle time per sample and a 1µL sample injection. To increase throughput, we used a dual column set up to equilibrate the second column while the first is running a sample. The sample analytical gradient was as follows: starting with a flow rate of 0.4mL/minute at 15% B and increasing to 50% B over 2.5 minutes, then to 57% over 0.1 minutes, to 70% over 6.4 minutes, to 93% over 0.1 minute, to 96% over 1.9 minutes and finally to 100% over 0.1 minute. The solvent was then held at 100% B for 0.9 minutes (total 12.0 minutes). Equilibration was started as follows: solvent was decreased from 100% B to 15% B over 0.2 minutes and held until a total of 16 minutes. The next sample is injected and the columns are switched. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) |
| Column Temperature: | 45 |
| Flow Gradient: | Starting with a flow rate of 0.4mL/minute at 15% B and increasing to 50% B over 2.5 minutes, then to 57% over 0.1 minutes, to 70% over 6.4 minutes, to 93% over 0.1 minute, to 96% over 1.9 minutes and finally to 100% over 0.1 minute. The solvent was then held at 100% B for 0.9 minutes (total 12.0 minutes). Equilibration was started as follows: solvent was decreased from 100% B to 15% B over 0.2 minutes and held until a total of 16 minutes. |
| Flow Rate: | 0.4mL/min |
| Solvent A: | 50% water/30% acetonitrile/20% isopropanol; 10mM ammonium formate; 5uM medronic acid |
| Solvent B: | 1% water/9% acetonitrile/90% isopropanol; 10mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004569 |
| Analysis ID: | AN004823 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Details previously published in https://doi.org/10.1016/j.chembiol.2018.10.008 Analysis of plasma extracts was performed on an Agilent 6490 QQQ mass spectrometer with an Agilent 1290 series HPLC system and a ZORBAX eclipse plus C18 column (2.1x100mm 1.8μm, Agilent) with the thermostat set at 60°C. Mass spectrometry analysis was performed in positive ion mode with dynamic scheduled multiple reaction monitoring (MRM). Mass spectrometry settings and MRM transitions for each lipid class, subclass and individual species are shown in Tables 1 and S1. The solvent system consisted of solvent A) 50% H2O / 30% acetonitrile / 20% isopropanol (v/v/v) containing 10mM ammonium formate and solvent B) 1% H2O / 9% acetonitrile / 90% isopropanol (v/v/v) containing 10mM ammonium formate. We utilized a stepped linear gradient with a 15-minute cycle time per sample and a 1μL sample injection. The gradient was as follows; starting with a flow rate of 0.4ml/minute at 10% B and increasing to 45% B over 2.7 minutes, then to 53% over 0.1 minutes, to 65% over 6.2 minutes, to 89% over 0.1 minute, to 92% over 1.9 minutes and finally to 100% over 0.1 minute. The solvent was then held at 100% B for 0.8 minutes (total 11.9 minutes). Equilibration was as follows, solvent was decreased from 100% B to 10% B over 0.1 minute and held for an additional 0.9 minutes. Flow rate was then switched to 0.6 ml/minute for 1 minute before returning to 0.4 ml/minute over 0.1 minutes. Solvent B was held at 10% B for a further 0.9 minutes at 0.4ml/minutes for a total cycle time of 15 minutes. The following mass spectrometer conditions were used; gas temperature, 150°C, gas flow rate 17L/min, nebulizer 20psi, Sheath gas temperature 200°C, capillary voltage 3500V and sheath gas flow 10L/min. Isolation widths for Q1 and Q3 were set to “unit” resolution (0.7 amu). PQC samples consisting of a pooled set of 6 healthy individuals were incorporated into the analysis at 1 PQC per 18 plasma samples. TQC consisted of PQC extracts which were pooled and split into individual vials to provide a measure of technical variation from the mass spectrometer only. These were included at a ratio of 1 TQC per 18 plasma samples. TQCs were monitored for changes in peak area, width and retention time to determine the performance of the LC-MS/MS analysis and were subsequently used to align for differential responses across the analytical batches. |
| Ion Mode: | POSITIVE |
