Summary of Study ST002453

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 PR001580. The data can be accessed directly via it's Project DOI: 10.21228/M8G711 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	ST002453
Study Title	APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge (Part 3 of 3)
Study Summary	The E4 allele of Apolipoprotein E (APOE) is associated with both metabolic dysfunction and a heightened pro-inflammatory response – two findings that may be intrinsically linked through the concept of immunometabolism. Here, we combined bulk, single-cell, and spatial transcriptomics with cell-specific and spatially resolved metabolic analyses to systematically address the role of APOE across age, neuroinflammation, and AD pathology. RNAseq highlighted immunometabolic changes across the APOE4 glial transcriptome, specifically in subsets of metabolically distinct microglia enriched in the E4 brain during aging or following an inflammatory challenge. E4 microglia display increased Hif1α expression, a disrupted TCA cycle, and are inherently pro-glycolytic, while spatial transcriptomics and MALDI mass spectrometry imaging highlight an E4-specific response to amyloid that is characterized by widespread alterations in lipid metabolism. Taken together, our findings emphasize a central role for APOE in regulating microglial immunometabolism.
Institute	University of Kentucky
Department	Physiology
Laboratory	Lance Johnson; Josh Morganti
Last Name	Devanney
First Name	Nicholas
Address	Physiology, 760 Press Ave, Healthy Kentucky Research Bldg, Rm152, Lexington, Kentucky, 40508, USA
Email	Nicholas.Devanney@uky.edu
Phone	8593238083
Submit Date	2022-11-14
Raw Data Available	Yes
Raw Data File Type(s)	raw(Waters)
Analysis Type Detail	MALDI-MS
Release Date	2023-01-25
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001580
Project DOI:	doi: 10.21228/M8G711
Project Title:	APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge
Project Summary:	The E4 allele of Apolipoprotein E (APOE) is associated with both metabolic dysfunction and a heightened pro-inflammatory response – two findings that may be intrinsically linked through the concept of immunometabolism. Here, we combined bulk, single-cell, and spatial transcriptomics with cell-specific and spatially resolved metabolic analyses to systematically address the role of APOE across age, neuroinflammation, and AD pathology. RNAseq highlighted immunometabolic changes across the APOE4 glial transcriptome, specifically in subsets of metabolically distinct microglia enriched in the E4 brain during aging or following an inflammatory challenge. E4 microglia display increased Hif1α expression, a disrupted TCA cycle, and are inherently pro-glycolytic, while spatial transcriptomics and MALDI mass spectrometry imaging highlight an E4-specific response to amyloid that is characterized by widespread alterations in lipid metabolism. Taken together, our findings emphasize a central role for APOE in regulating microglial immunometabolism.
Institute:	University of Kentucky, Department of Physiology
Last Name:	Devanney
First Name:	Nicholas
Address:	Physiology, 760 Press Ave, Healthy Kentucky Research Bldg, Rm152, Lexington, Kentucky, 40508, USA
Email:	Nicholas.Devanney@uky.edu
Phone:	8593238083
Project Comments:	Part 2 of 3

Subject:

Subject ID:	SU002542
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	APOE-targeted replacement mice homozygous for human E3 (B6.129P2-Apoe^tm2(APOE3)Mae N8, Taconic #1548-F) or human E4 (B6.129P2- Apoe^tm3(APOE4)Mae N8, Taconic #1549-F) alleles and crossed to the 5x Familial Alzheimer's Disease (5XFAD) model (MMRRC #34840, B6SJL^Tg( APPSwFlLon,PSEN1M146LL286V)6799Vas/Mmjax))
Age Or Age Range:	3 months, 12 months, 24 months
Gender:	Female

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Brain Region	Group	APOE genotype	5XFAD Genotype	Age
SA245312	JJ3_73_Cerebral Nuclei	Cerebral Nuclei	E3_FAD	E3/E3	Hemizygous	12 months
SA245313	JJ3_76_Cerebral Nuclei	Cerebral Nuclei	E3_FAD	E3/E3	Hemizygous	12 months
SA245314	JJ3_66_Cerebral Nuclei	Cerebral Nuclei	E3_FAD	E3/E3	Hemizygous	12 months
SA245315	B427_Cerebral Nuclei	Cerebral Nuclei	E3_old	E3/E3	Wild-type	24 months
SA245316	B354_Cerebral Nuclei	Cerebral Nuclei	E3_old	E3/E3	Wild-type	24 months
SA245317	B425_Cerebral Nuclei	Cerebral Nuclei	E3_old	E3/E3	Wild-type	24 months
SA245318	B647_Cerebral Nuclei	Cerebral Nuclei	E3_young	E3/E3	Wild-type	3 months
SA245319	B648_Cerebral Nuclei	Cerebral Nuclei	E3_young	E3/E3	Wild-type	3 months
SA245320	B652_Cerebral Nuclei	Cerebral Nuclei	E3_young	E3/E3	Wild-type	3 months
SA245321	KK4_116_Cerebral Nuclei	Cerebral Nuclei	E4_FAD	E4/E4	Hemizygous	12 months
SA245322	KK4_96_Cerebral Nuclei	Cerebral Nuclei	E4_FAD	E4/E4	Hemizygous	12 months
SA245323	KK4_40_Cerebral Nuclei	Cerebral Nuclei	E4_FAD	E4/E4	Hemizygous	12 months
SA245324	C202_Cerebral Nuclei	Cerebral Nuclei	E4_old	E4/E4	Wild-type	24 months
SA245325	C384_Cerebral Nuclei	Cerebral Nuclei	E4_old	E4/E4	Wild-type	24 months
SA245326	C362_Cerebral Nuclei	Cerebral Nuclei	E4_old	E4/E4	Wild-type	24 months
SA245327	C763_Cerebral Nuclei	Cerebral Nuclei	E4_young	E4/E4	Wild-type	3 months
SA245328	C762_Cerebral Nuclei	Cerebral Nuclei	E4_young	E4/E4	Wild-type	3 months
SA245329	C761_Cerebral Nuclei	Cerebral Nuclei	E4_young	E4/E4	Wild-type	3 months
SA245330	JJ3_73_Cortical Subplate	Cortical Subplate	E3_FAD	E3/E3	Hemizygous	12 months
SA245331	JJ3_76_Cortical Subplate	Cortical Subplate	E3_FAD	E3/E3	Hemizygous	12 months
SA245332	JJ3_66_Cortical Subplate	Cortical Subplate	E3_FAD	E3/E3	Hemizygous	12 months
SA245333	B425_Cortical Subplate	Cortical Subplate	E3_old	E3/E3	Wild-type	24 months
SA245334	B354_Cortical Subplate	Cortical Subplate	E3_old	E3/E3	Wild-type	24 months
SA245335	B427_Cortical Subplate	Cortical Subplate	E3_old	E3/E3	Wild-type	24 months
SA245336	B647_Cortical Subplate	Cortical Subplate	E3_young	E3/E3	Wild-type	3 months
SA245337	B648_Cortical Subplate	Cortical Subplate	E3_young	E3/E3	Wild-type	3 months
SA245338	B652_Cortical Subplate	Cortical Subplate	E3_young	E3/E3	Wild-type	3 months
SA245339	KK4_96_Cortical Subplate	Cortical Subplate	E4_FAD	E4/E4	Hemizygous	12 months
SA245340	KK4_116_Cortical Subplate	Cortical Subplate	E4_FAD	E4/E4	Hemizygous	12 months
SA245341	KK4_40_Cortical Subplate	Cortical Subplate	E4_FAD	E4/E4	Hemizygous	12 months
SA245342	C202_Cortical Subplate	Cortical Subplate	E4_old	E4/E4	Wild-type	24 months
SA245343	C362_Cortical Subplate	Cortical Subplate	E4_old	E4/E4	Wild-type	24 months
SA245344	C384_Cortical Subplate	Cortical Subplate	E4_old	E4/E4	Wild-type	24 months
SA245345	C763_Cortical Subplate	Cortical Subplate	E4_young	E4/E4	Wild-type	3 months
SA245346	C762_Cortical Subplate	Cortical Subplate	E4_young	E4/E4	Wild-type	3 months
SA245347	C761_Cortical Subplate	Cortical Subplate	E4_young	E4/E4	Wild-type	3 months
SA245348	JJ3_66_Fiber Tracts	Fiber Tracts	E3_FAD	E3/E3	Hemizygous	12 months
SA245349	JJ3_73_Fiber Tracts	Fiber Tracts	E3_FAD	E3/E3	Hemizygous	12 months
SA245350	JJ3_76_Fiber Tracts	Fiber Tracts	E3_FAD	E3/E3	Hemizygous	12 months
SA245351	B427_Fiber Tracts	Fiber Tracts	E3_old	E3/E3	Wild-type	24 months
SA245352	B425_Fiber Tracts	Fiber Tracts	E3_old	E3/E3	Wild-type	24 months
SA245353	B354_Fiber Tracts	Fiber Tracts	E3_old	E3/E3	Wild-type	24 months
SA245354	B648_Fiber Tracts	Fiber Tracts	E3_young	E3/E3	Wild-type	3 months
SA245355	B647_Fiber Tracts	Fiber Tracts	E3_young	E3/E3	Wild-type	3 months
SA245356	B652_Fiber Tracts	Fiber Tracts	E3_young	E3/E3	Wild-type	3 months
SA245357	KK4_40_Fiber Tracts	Fiber Tracts	E4_FAD	E4/E4	Hemizygous	12 months
SA245358	KK4_116_Fiber Tracts	Fiber Tracts	E4_FAD	E4/E4	Hemizygous	12 months
SA245359	KK4_96_Fiber Tracts	Fiber Tracts	E4_FAD	E4/E4	Hemizygous	12 months
SA245360	C384_Fiber Tracts	Fiber Tracts	E4_old	E4/E4	Wild-type	24 months
SA245361	C202_Fiber Tracts	Fiber Tracts	E4_old	E4/E4	Wild-type	24 months
SA245362	C362_Fiber Tracts	Fiber Tracts	E4_old	E4/E4	Wild-type	24 months
SA245363	C762_Fiber Tracts	Fiber Tracts	E4_young	E4/E4	Wild-type	3 months
SA245364	C763_Fiber Tracts	Fiber Tracts	E4_young	E4/E4	Wild-type	3 months
SA245365	C761_Fiber Tracts	Fiber Tracts	E4_young	E4/E4	Wild-type	3 months
SA245366	JJ3_66_Hippocampus	Hippocampus	E3_FAD	E3/E3	Hemizygous	12 months
SA245367	JJ3_73_Hippocampus	Hippocampus	E3_FAD	E3/E3	Hemizygous	12 months
SA245368	JJ3_76_Hippocampus	Hippocampus	E3_FAD	E3/E3	Hemizygous	12 months
SA245369	B425_Hippocampus	Hippocampus	E3_old	E3/E3	Wild-type	24 months
SA245370	B354_Hippocampus	Hippocampus	E3_old	E3/E3	Wild-type	24 months
SA245371	B427_Hippocampus	Hippocampus	E3_old	E3/E3	Wild-type	24 months
SA245372	B652_Hippocampus	Hippocampus	E3_young	E3/E3	Wild-type	3 months
SA245373	B647_Hippocampus	Hippocampus	E3_young	E3/E3	Wild-type	3 months
SA245374	B648_Hippocampus	Hippocampus	E3_young	E3/E3	Wild-type	3 months
SA245375	KK4_116_Hippocampus	Hippocampus	E4_FAD	E4/E4	Hemizygous	12 months
SA245376	KK4_96_Hippocampus	Hippocampus	E4_FAD	E4/E4	Hemizygous	12 months
SA245377	KK4_40_Hippocampus	Hippocampus	E4_FAD	E4/E4	Hemizygous	12 months
SA245378	C384_Hippocampus	Hippocampus	E4_old	E4/E4	Wild-type	24 months
SA245379	C202_Hippocampus	Hippocampus	E4_old	E4/E4	Wild-type	24 months
SA245380	C362_Hippocampus	Hippocampus	E4_old	E4/E4	Wild-type	24 months
SA245381	C761_Hippocampus	Hippocampus	E4_young	E4/E4	Wild-type	3 months
SA245382	C762_Hippocampus	Hippocampus	E4_young	E4/E4	Wild-type	3 months
SA245383	C763_Hippocampus	Hippocampus	E4_young	E4/E4	Wild-type	3 months
SA245384	JJ3_76_Hypothalamus	Hypothalamus	E3_FAD	E3/E3	Hemizygous	12 months
SA245385	JJ3_73_Hypothalamus	Hypothalamus	E3_FAD	E3/E3	Hemizygous	12 months
SA245386	JJ3_66_Hypothalamus	Hypothalamus	E3_FAD	E3/E3	Hemizygous	12 months
SA245387	B425_Hypothalamus	Hypothalamus	E3_old	E3/E3	Wild-type	24 months
SA245388	B354_Hypothalamus	Hypothalamus	E3_old	E3/E3	Wild-type	24 months
SA245389	B427_Hypothalamus	Hypothalamus	E3_old	E3/E3	Wild-type	24 months
SA245390	B647_Hypothalamus	Hypothalamus	E3_young	E3/E3	Wild-type	3 months
SA245391	B648_Hypothalamus	Hypothalamus	E3_young	E3/E3	Wild-type	3 months
SA245392	B652_Hypothalamus	Hypothalamus	E3_young	E3/E3	Wild-type	3 months
SA245393	KK4_116_Hypothalamus	Hypothalamus	E4_FAD	E4/E4	Hemizygous	12 months
SA245394	KK4_96_Hypothalamus	Hypothalamus	E4_FAD	E4/E4	Hemizygous	12 months
SA245395	KK4_40_Hypothalamus	Hypothalamus	E4_FAD	E4/E4	Hemizygous	12 months
SA245396	C384_Hypothalamus	Hypothalamus	E4_old	E4/E4	Wild-type	24 months
SA245397	C202_Hypothalamus	Hypothalamus	E4_old	E4/E4	Wild-type	24 months
SA245398	C362_Hypothalamus	Hypothalamus	E4_old	E4/E4	Wild-type	24 months
SA245399	C763_Hypothalamus	Hypothalamus	E4_young	E4/E4	Wild-type	3 months
SA245400	C761_Hypothalamus	Hypothalamus	E4_young	E4/E4	Wild-type	3 months
SA245401	C762_Hypothalamus	Hypothalamus	E4_young	E4/E4	Wild-type	3 months
SA245402	JJ3_73_Iso Cortex	Iso Cortex	E3_FAD	E3/E3	Hemizygous	12 months
SA245403	JJ3_76_Iso Cortex	Iso Cortex	E3_FAD	E3/E3	Hemizygous	12 months
SA245404	JJ3_66_Iso Cortex	Iso Cortex	E3_FAD	E3/E3	Hemizygous	12 months
SA245405	B427_Iso Cortex	Iso Cortex	E3_old	E3/E3	Wild-type	24 months
SA245406	B425_Iso Cortex	Iso Cortex	E3_old	E3/E3	Wild-type	24 months
SA245407	B354_Iso Cortex	Iso Cortex	E3_old	E3/E3	Wild-type	24 months
SA245408	B647_Iso Cortex	Iso Cortex	E3_young	E3/E3	Wild-type	3 months
SA245409	B652_Iso Cortex	Iso Cortex	E3_young	E3/E3	Wild-type	3 months
SA245410	B648_Iso Cortex	Iso Cortex	E3_young	E3/E3	Wild-type	3 months
SA245411	KK4_96_Iso Cortex	Iso Cortex	E4_FAD	E4/E4	Hemizygous	12 months

Showing page 1 of 2 Results: 1 2 Next Showing results 1 to 100 of 162

Collection:

Collection ID:	CO002535
Collection Summary:	Three different mice for each experimental group (18 mice in total) were anesthetized via 5.0% isoflurane before exsanguination and transcardial perfusion with ice-cold Dulbecco’s phosphate buffered saline (DPBS; Gibco # 14040133). Following perfusion, hemibrains were quickly removed, leaving behind brainstem and cerebellum. Hemibrains were immediately placed in OCT compound (Fisher HealthCare Tissue Plus O.C.T. Compound Clear 4585) and gently lowered into isopentane (Sigma-Aldrich 2- Methylbutane M32631) in a beaker surrounded by dry ice (isopentane chilled to approximately -70°C). Hemibrains were submerged for 60 seconds, placed on dry ice, wrapped in aluminum foil, and stored at -80°C until sectioning.
Sample Type:	Brain

Treatment:

Treatment ID:	TR002554
Treatment Summary:	All mice were group housed in sterile micro-isolator cages (Lab Products, Maywood, NJ), and fed autoclaved food and acidified water ad libitum. No additional treatment was applied, with the only comparisons being across different genotypes and ages as specified in the study design table.

Sample Preparation:

Sampleprep ID:	SP002548
Sampleprep Summary:	Prepared brain hemispheres were cryosectioned to 10 μm thick coronal sections at approximately Bregma -2.00 mm. Brain sections were mounted on glass slides and prepared for MALDI MSI as follows: After desiccation for one hour, slides were sprayed with 14 passes of 7mg/mL N-(1-Naphthyl) ethylenediamine dihydrochloride (NEDC) matrix (Sigma) in 70% methanol (HPLC-grade, Sigma) which was applied at 0.06mL/min with a 3mm offset and a velocity of 1200mm/min at 30°C and 10psi using the M5 Sprayer with a heated tray of 50°C. Slides were used immediately or stored in a desiccator until analysis.

Sampleprep ID:

SP002548

Sampleprep Summary:

Prepared brain hemispheres were cryosectioned to 10 μm thick coronal sections at approximately Bregma -2.00 mm. Brain sections were mounted on glass slides and prepared for MALDI MSI as follows: After desiccation for one hour, slides were sprayed with 14 passes of 7mg/mL N-(1-Naphthyl) ethylenediamine dihydrochloride (NEDC) matrix (Sigma) in 70% methanol (HPLC-grade, Sigma) which was applied at 0.06mL/min with a 3mm offset and a velocity of 1200mm/min at 30°C and 10psi using the M5 Sprayer with a heated tray of 50°C. Slides were used immediately or stored in a desiccator until analysis.

Combined analysis:

Analysis ID	AN004002
Analysis type	MS
Chromatography type	None (Direct infusion)
Chromatography system	none
Column	none
MS Type	MALDI
MS instrument type	QTOF
MS instrument name	Waters Synapt G2 XS
Ion Mode	NEGATIVE
Units	Intensity per pixel

Chromatography:

Chromatography ID:	CH002955
Chromatography Summary:	Not applicable (MALDI MSI)
Instrument Name:	none
Column Name:	none
Column Temperature:	N/A
Flow Gradient:	N/A
Flow Rate:	N/A
Solvent A:	N/A
Solvent B:	N/A
Chromatography Type:	None (Direct infusion)

MS:

MS ID:	MS003750
Analysis ID:	AN004002
Instrument Name:	Waters Synapt G2 XS
Instrument Type:	QTOF
MS Type:	MALDI
MS Comments:	For the detection of lipids, a Waters SynaptG2-Xs high-definition mass spectrometer equipped with traveling wave ion mobility was employed with the following parameters. The laser was operating at 2000 Hz with an energy of 300 AU and spot size of 50 μm at X and Y coordinates of 100μm with mass range set at 50 – 1000 m/z in negative mode. MALDI-MSI data files were processed to adjust for mass drift during the MALDI scan and to enhance image quality and improve signal-tonoise ratio using an algorithm available within the High-Definition Imaging (HDI) software (Waters Corp). To adjust for mass drift during the MALDI scan, raw files were processed using a carefully curated list of 20 MALDI NEDC matrix peaks (m/z), 26 small molecule MALDI peaks(m/z), and 24 lipid peaks(m/z). Files were processed at a sample duration of 10 sec at a frequency rate of 0.5 min, and an m/z window of 0.1 Da, using an internal lock mass of previously defined metabolite of taurine 124.007 m/z with a tolerance of 1amu and a minimum signal intensity of 100,000 counts. Data acquisition spectrums were uploaded to the HDI software for the generation of lipid images. Regions of interest (ROIs) were user defined by a blinded investigator using anatomical reference points based on the mouse Allen Brain atlas. For all pixels defined within a ROI, peak intensities were averaged and normalized by total ion current (TIC) and number of pixels.
Ion Mode:	NEGATIVE