Summary of Study ST001936

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 PR001225. The data can be accessed directly via it's Project DOI: 10.21228/M8C69S This work is supported by NIH grant, U2C- DK119886.

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Study IDST001936
Study TitlePseudoexfoliation aqueous humor lipidome suggests enrichment of specific pathways
Study SummaryPseudoexfoliation syndrome (PEX) is systemic disorder that manifests as white, fluffy, proteinaceous fibrillar material throughout the body. In the eye such deposits result in Pseudoexfoliation glaucoma (PEXG), due to impeding aqueous humor outflow. Serum lipid alterations and increased lipid peroxidation have been reported in PEX. We report first ever comprehensive lipid profiling of the aqueous humor (AH) of PEXG. Our untargeted lipidomic analysis of 23 non-glaucomatous control, 19 primary open angle glaucoma, 9 PEX, and 14 PEXG AH with 13 deuterated lipid internal standards for normalization among the lipid classes resulted in the combined identification of 489 lipid species within 26 lipid classes across PEX, PEXG, POAG, and control AH. The mean total lipid content in the AH across samples showed that control AH (mean peak area 13.54 ± 56.1) had, on average, greater total lipid content than PEX (4.21 ± 10.90), PEXG (9.08 ± 25.97), and POAG (5.66 ± 15.75) samples. Multiple cholesterol esters (ChE), phosphatidylcholines (PC), triglycerides (TG), and ceramides (Cer) were present in higher concentrations for the PEXG AH samples. Some of the lipids found in high concentrations in the PEXG samples are ChE(16:0), ChE(20:3), ChE(18:1), ChE(18:3), ChE(22:6), ChE(18:2), ChE(20:4), PC(16:0/16:0), PC(16:0/18:2), TG(18:1/18:1/20:4), and Cer(t18:0/24:0). The CerG2GNAc1(d34:1) was enriched in control samples and depleted both in PEX and PEXG samples. The PC (18:0/18:2), PC (36:2), and PC (34:1e) are in low concentrations for PEX but highly concentrated in PEXG, despite both having similar material deposits, suggesting they are fundamentally different in composition. Elevations in Apolipoprotein A-I (APOA1) correlated to increase abundance of PC lipid species in the AH of patients with PEXG. Machine learning prediction with three supervised logistic regression binary classification tasks showed 1) POAG vs control, with 86% accuracy 2) PEXG vs control, with 71% accuracy and 3) PEX vs control, with 86% accuracy, respectively.
Institute
University of Miami
DepartmentOphthalmology
Last NameBhattacharya
First NameSanjoy K.
Address1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Emailsbhattacharya@med.miami.edu
Phone3054824103
Submit Date2021-09-16
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-11-04
Release Version1
Sanjoy K. Bhattacharya Sanjoy K. Bhattacharya
https://dx.doi.org/10.21228/M8C69S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001225
Project DOI:doi: 10.21228/M8C69S
Project Title:Pseudoexfoliation aqueous humor lipidome suggests enrichment of specific pathways
Project Summary:Lipids were identified and quantified with LipidSearch 4.2.21. Statistical analysis was conducted through MetaboAnalyst 5.0.
Institute:University of Miami
Department:Ophthalmology
Last Name:Bhattacharya
First Name:Sanjoy K.
Address:1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Email:sbhattacharya@med.miami.edu
Phone:3054824103

Subject:

Subject ID:SU003116
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Factor
SA326749N17Control
SA326750N16Control
SA326751N15Control
SA326752N14Control
SA326753N18Control
SA326754N19Control
SA326755N23Control
SA326756N22Control
SA326757N21Control
SA326758N20Control
SA326759N13Control
SA326760N12Control
SA326761N2Control
SA326762N3Control
SA326763N5Control
SA326764N6Control
SA326765N1Control
SA326766N8Control
SA326767N11Control
SA326768N10Control
SA326769N9Control
SA326770N24Control
SA326771N7Control
SA326772PX18PEX
SA326773BB03PEX
SA326774BB04PEX
SA326775PX13PEX
SA326776PX12PEX
SA326777PX1PEX
SA326778PX5PEX
SA326779PX3PEX
SA326780PX10PEX
SA326781PX2PEXG
SA326782BB02PEXG
SA326783PX4PEXG
SA326784PX7PEXG
SA326785PX16PEXG
SA326786PX17PEXG
SA326787PX19PEXG
SA326788PX20PEXG
SA326789PX15PEXG
SA326790PX14PEXG
SA326791PX8PEXG
SA326792PX9PEXG
SA326793PX11PEXG
SA326794PX6PEXG
SA326795G10POAG
SA326796G6POAG
SA326797G7POAG
SA326798G8POAG
SA326799G5POAG
SA326800G4POAG
SA326801G1POAG
SA326802G2POAG
SA326803G3POAG
SA326804G9POAG
SA326805G11POAG
SA326806G16POAG
SA326807G17POAG
SA326808G18POAG
SA326809G15POAG
SA326810G14POAG
SA326811G12POAG
SA326812G13POAG
SA326813N4POAG
Showing results 1 to 65 of 65

Collection:

Collection ID:CO003109
Collection Summary:All AH samples collected came from human donors during cataract surgery. A total of 66 samples were collected which included non-glaucomatous controls and those with pseudoexfoliation syndrome (PEX), pseudoexfoliation glaucoma (PEXG), and primary open-angle glaucoma (POAG). The clinicians provided samples from the Department of Ophthalmology of Hospital Clínico San Carlos in Madrid, Spain. The patient samples consisted of 19 POAG, 9 PEX, 14 PEXG, and 23 controls.
Sample Type:Eye tissue

Treatment:

Treatment ID:TR003125
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP003122
Sampleprep Summary:Lipids were extracted from POAG, PEX, PEXG, and control AH samples using the Bligh and Dyer method (Bligh and Dyer, 1959). EquiSPLASHTM Lipidomix quantitative mass spec internal standard was spiked into each sample to normalize the lipids. For the extraction, a 2:1 chloroform:methanol solution with 100 µL of water was added to promote phase separation followed by centrifugation at four °C at 14,000 rpm for 20 minutes. After centrifugation, separation was observed and the extracted lipids were collected from the lower, organic chloroform phase with a syringe. Once the lipids were isolated and transferred to 2 mL glass vials, they were dried in a Speed-Vac for about 90 minutes. The upper, aqueous, water/methanol phase containing most of the proteins was collected and stored for a Bradford protein assay to measure protein concentration in the future. When the samples were dehydrated, they were flushed with argon gas for storage at -80°C until ready for mass spec analysis. To prepare the samples for mass spec analysis, the dried lipids were resuspended in a 1:1 acetonitrile:isopropyl alcohol solution, sonicated for 30 minutes, and aliquoted into mass spec vials.

Combined analysis:

Analysis ID AN004932
Analysis type MS
Chromatography type Reversed phase
Chromatography system Vanquish Horizon Binary UHPLC
Column Accucore Vanquish C18+ UHPLC (2.1mm x 150mm x 1.5µm)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units µg/mL

Chromatography:

Chromatography ID:CH003722
Instrument Name:Vanquish Horizon Binary UHPLC
Column Name:Accucore Vanquish C18+ UHPLC (2.1mm x 150mm x 1.5µm)
Chromatography Type:Reversed phase

MS:

MS ID:MS004675
Analysis ID:AN004932
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Lipids were identified and quantified with LipidSearch 4.2.21. Statistical analysis was conducted through MetaboAnalyst 5.0.
Ion Mode:UNSPECIFIED
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