Summary of Study ST002928

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 PR001821. The data can be accessed directly via it's Project DOI: 10.21228/M8B725 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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST002928
Study TitleThe major TMEM106B dementia risk allele affects TMEM106B protein levels, fibril formation, and myelin lipid homeostasis in the ageing human hippocampus
Study SummaryBackground: The risk for dementia increases exponentially from the seventh decade of life. Identifying and understanding the biochemical changes that sensitize the ageing brain to neurodegeneration will provide new opportunities for dementia prevention and treatment. This study aimed to determine how ageing and major genetic risk factors for dementia affect the hippocampal proteome and lipidome of neurologically-normal humans over the age of 65. The hippocampus was chosen as it is highly susceptible to atrophy with ageing and in several neurodegenerative diseases. Methods: Mass spectrometry-based proteomic and lipidomic analysis of CA1 hippocampus samples from 74 neurologically normal human donors, aged 66 – 104, was used in combination with multiple regression models and gene set enrichment analysis to identify age-dependent changes in the proteome and lipidome. ANOVA was used to test the effect of major dementia risk alleles in the TMEM106B and APOE genes on the hippocampal proteome and lipidome, adjusting for age, gender, and post-mortem interval. Fibrillar C-terminal TMEM106B fragments were isolated using sarkosyl fractionation and quantified by immunoblotting. Results: Forty proteins were associated with age at false discovery rate-corrected P<0.05, including proteins that regulate cell adhesion, the cytoskeleton, amino acid and lipid metabolism, and ribosomal subunits. TMEM106B, a regulator of lysosomal and oligodendrocyte function, was regulated with greatest effect size. The increase in TMEM106B levels with ageing was specific to carriers of the rs1990622-A allele in the TMEM106B gene that increases risk for frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, and hippocampal sclerosis with ageing. Rs1990622-A was also associated with higher TMEM106B fibril content. Hippocampal lipids were not significantly affected by APOE genotype, however levels of myelin-enriched sulfatides and hexosylceramides were significantly lower, and polyunsaturated phospholipids were higher, in rs1990622-A carriers after controlling for APOE genotype. Conclusions: Our study demonstrates that TMEM106B protein abundance is increased with brain ageing in humans, establishes that dementia risk allele rs1990622-A predisposes to TMEM106B fibril formation in the hippocampus, and provides the first evidence that rs1990622-A affects brain lipid homeostasis, particularly myelin lipids. Our data suggests that TMEM106B is one of a growing list of major dementia risk genes that affect glial lipid metabolism.
Institute
University of Sydney
Last NameLee
First NameJUN YUP
AddressJohn Hopkins Dr, Camperdown NSW 2050
Emailjlee4934@uni.sydney.edu.au
Phone0401042970
Submit Date2023-07-18
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-11-05
Release Version1
JUN YUP Lee JUN YUP Lee
https://dx.doi.org/10.21228/M8B725
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001821
Project DOI:doi: 10.21228/M8B725
Project Title:The major TMEM106B dementia risk allele affects TMEM106B protein levels, fibril formation, and myelin lipid homeostasis in the ageing human hippocampus
Project Summary:Background: The risk for dementia increases exponentially from the seventh decade of life. Identifying and understanding the biochemical changes that sensitize the ageing brain to neurodegeneration will provide new opportunities for dementia prevention and treatment. This study aimed to determine how ageing and major genetic risk factors for dementia affect the hippocampal proteome and lipidome of neurologically-normal humans over the age of 65. The hippocampus was chosen as it is highly susceptible to atrophy with ageing and in several neurodegenerative diseases. Methods: Mass spectrometry-based proteomic and lipidomic analysis of CA1 hippocampus samples from 74 neurologically normal human donors, aged 66 – 104, was used in combination with multiple regression models and gene set enrichment analysis to identify age-dependent changes in the proteome and lipidome. ANOVA was used to test the effect of major dementia risk alleles in the TMEM106B and APOE genes on the hippocampal proteome and lipidome, adjusting for age, gender, and post-mortem interval. Fibrillar C-terminal TMEM106B fragments were isolated using sarkosyl fractionation and quantified by immunoblotting. Results: Forty proteins were associated with age at false discovery rate-corrected P<0.05, including proteins that regulate cell adhesion, the cytoskeleton, amino acid and lipid metabolism, and ribosomal subunits. TMEM106B, a regulator of lysosomal and oligodendrocyte function, was regulated with greatest effect size. The increase in TMEM106B levels with ageing was specific to carriers of the rs1990622-A allele in the TMEM106B gene that increases risk for frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, and hippocampal sclerosis with ageing. Rs1990622-A was also associated with higher TMEM106B fibril content. Hippocampal lipids were not significantly affected by APOE genotype, however levels of myelin-enriched sulfatides and hexosylceramides were significantly lower, and polyunsaturated phospholipids were higher, in rs1990622-A carriers after controlling for APOE genotype. Conclusions: Our study demonstrates that TMEM106B protein abundance is increased with brain ageing in humans, establishes that dementia risk allele rs1990622-A predisposes to TMEM106B fibril formation in the hippocampus, and provides the first evidence that rs1990622-A affects brain lipid homeostasis, particularly myelin lipids. Our data suggests that TMEM106B is one of a growing list of major dementia risk genes that affect glial lipid metabolism.
Institute:University of Sydney
Department:Faculty of Medicine and Health
Last Name:Lee
First Name:JUN YUP
Address:John Hopkins Dr, Camperdown NSW 2050
Email:jlee4934@uni.sydney.edu.au
Phone:0401042970

Subject:

Subject ID:SU003041
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 APOE genotype TMEM SNP
SA31792421e2/e2 A/G
SA31792534e2/e2 A/G
SA31792632e2/e3 A/G
SA31792769e2/e3 A/G
SA31792835e2/e3 A/G
SA31792960e2/e3 A/G
SA31793046e2/e3 A/G
SA31793180e2/e3 A/G
SA3179322e2/e3 A/G
SA31793329e2/e3 G/G
SA3179349e2/e3 G/G
SA31793559e2/e3 NA
SA31793645e2/e4 A/A
SA3179378e2/e4 A/G
SA31793853e2/e4 G/G
SA31793961e2/e4 G/G
SA31794030e3/e3 A/A
SA31794136e3/e3 A/A
SA31794250e3/e3 A/A
SA31794356e3/e3 A/A
SA31794437e3/e3 A/A
SA31794533e3/e3 A/A
SA31794662e3/e3 A/A
SA31794716e3/e3 A/A
SA31794813e3/e3 A/A
SA31794975e3/e3 A/A
SA31795076e3/e3 A/A
SA31795118e3/e3 A/A
SA31795271e3/e3 A/A
SA31795322e3/e3 A/A
SA31795467e3/e3 A/A
SA31795551e3/e3 A/G
SA31795678e3/e3 A/G
SA31795752e3/e3 A/G
SA31795864e3/e3 A/G
SA31795955e3/e3 A/G
SA31796048e3/e3 A/G
SA31796173e3/e3 A/G
SA31796258e3/e3 A/G
SA31796368e3/e3 A/G
SA31796474e3/e3 A/G
SA31796541e3/e3 A/G
SA31796638e3/e3 A/G
SA3179677e3/e3 A/G
SA31796847e3/e3 A/G
SA31796919e3/e3 A/G
SA3179706e3/e3 A/G
SA31797127e3/e3 A/G
SA31797212e3/e3 A/G
SA31797344e3/e3 A/G
SA3179745e3/e3 A/G
SA31797542e3/e3 A/G
SA31797657e3/e3 G/G
SA31797711e3/e3 G/G
SA31797820e3/e3 G/G
SA31797917e3/e3 G/G
SA31798066e3/e3 G/G
SA31798124e3/e3 G/G
SA31798215e3/e3 G/G
SA31798310e3/e3 G/G
SA31798426e3/e3 G/G
SA31798579e3/e3 G/G
SA31798677e3/e3 NA
SA31798731e3/e3 NA
SA31798823e3/e4 A/A
SA3179891e3/e4 A/A
SA31799070e3/e4 A/A
SA31799154e3/e4 A/G
SA31799249e3/e4 A/G
SA31799325e3/e4 A/G
SA31799463e3/e4 A/G
SA31799514e3/e4 A/G
SA31799639e3/e4 A/G
SA31799743e3/e4 G/G
SA31799828e3/e4 G/G
SA31799965e3/e4 G/G
Showing results 1 to 76 of 76

Collection:

Collection ID:CO003034
Collection Summary:Homogenates were prepared by placing 10-20 mg of frozen tissue into 500 L of 20 mM Hepes pH 7.4, 10 mM KCl, EDTA-free cOmplete protease inhibitor cocktail (Roche), 1 mM dithiothreitol, and 3 mM β-glycerophosphate, and ultrasonicating for 5 min (30 s on/30 s off) at 4 °C in a Qsonica Q800R2 sonicating bath. Homogenates were cleared by centrifugation at 1000g for 10 min at 4 °C, and the supernatant was stored at -80 °C in 100 µL aliquots. Total protein concentrations were determined using the Bradford assay (Bio-Rad). Lipids were extracted from hippocampal homogenates (~100 µg protein) using a one phase butanol-methanol (BUME) (1:1 v/v) procedure [34]. The following internal standards were added to each sample: 5 nmoles of d19:0/19:0 PC, 2 nmoles of d18:1/17:0 SM, d18:1/12:0 HexCer, 17:0/17:0 PS, 17:0/17:0 PE, 17:0/17:0/17:0 TG, 17:0/17:0 PG, 14:0/14:0/14:0/14:0 cardiolipin, 17:0 cholesteryl ester, 1 nmole of 17:0/17:0 PA, d18:1/15:0-d7 PI, cholesterol-d7, 0.5 nmoles of d18:1/17:0 ST, d18:1/17:0 ceramide, 17:1 LPE, 17:1 LPS, 17:0 LPC, 18:1-d7 monoacylglycerol, d18:1/15:0-d7 diacylglycerol, d18:1/12:0 Hex2Cer, and 0.2 nmoles of 17:1 sphingosine, 17:1 sphingosine 1-phosphate, d3-16:0 acylcarnitine, 17:0 LPA.
Sample Type:Brain

Treatment:

Treatment ID:TR003050
Treatment Summary:No treatment. This study investigated the effects of age, TMEM106B rs1990622 SNP, and APOE genotype on the lipidome of CA1 hippocampus from physiologically ageing individuals.

Sample Preparation:

Sampleprep ID:SP003047
Sampleprep Summary:Lipids were extracted from hippocampal homogenates (~100 µg protein) using a one phase butanol-methanol (BUME) (1:1 v/v) procedure [34]. The following internal standards were added to each sample: 5 nmoles of d19:0/19:0 PC, 2 nmoles of d18:1/17:0 SM, d18:1/12:0 HexCer, 17:0/17:0 PS, 17:0/17:0 PE, 17:0/17:0/17:0 TG, 17:0/17:0 PG, 14:0/14:0/14:0/14:0 cardiolipin, 17:0 cholesteryl ester, 1 nmole of 17:0/17:0 PA, d18:1/15:0-d7 PI, cholesterol-d7, 0.5 nmoles of d18:1/17:0 ST, d18:1/17:0 ceramide, 17:1 LPE, 17:1 LPS, 17:0 LPC, 18:1-d7 monoacylglycerol, d18:1/15:0-d7 diacylglycerol, d18:1/12:0 Hex2Cer, and 0.2 nmoles of 17:1 sphingosine, 17:1 sphingosine 1-phosphate, d3-16:0 acylcarnitine, 17:0 LPA.

Combined analysis:

Analysis ID AN004802
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap
Ion Mode UNSPECIFIED
Units % Total

Chromatography:

Chromatography ID:CH003630
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:Run time was 25 min using a binary gradient starting at 20% B for 3 min, increasing to 45% B from 3 - 5.5 min, then to 65% B from 5.5 - 8 min, then to 85% B from 8 - 13 min, then to 100% B from 13 - 14 min. The gradient was held at 100% B from 14 - 20 min, then decreased to 20% B and held to 25 min.
Flow Rate:0.28 ml/min
Solvent A:60% acetonitrile/40% water; 10 mM ammonium formate; 0.1% formic acid
Solvent B:10% acetonitrile/90% isopropanol; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS004548
Analysis ID:AN004802
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Each sample injected twice, once in positive and once in negative.
Ion Mode:UNSPECIFIED
  logo