Summary of Study ST003614

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 PR002234. The data can be accessed directly via it's Project DOI: 10.21228/M8VJ9K This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST003614
Study Title	Kupffer cells control neonatal hepatic glucose metabolism via Igf1 signaling - lipidomics analysis of postnatal day 0 murine livers after macrophages depletion using Spi1 conditional KO
Study Type	lipidomics analysis of P0 livers from mice
Study Summary	During perinatal development, liver metabolism is tightly regulated to ensure energy supply for the newborn. Before birth, glycogen is stored in hepatocytes and later metabolized to glucose, meeting the energy demands of the neonate. Shortly after birth, lipogenesis begins, driven by the transcriptional activation of enzymes involved in fatty acid oxidation. These processes are thought to be largely regulated by systemic insulin and glucagon levels. However, the role of liver-derived local factors in neonatal hepatocyte metabolism remains unexplored. Kupffer cells (KCs), the liver’s resident macrophages, colonize the fetal liver early in embryogenesis and support liver metabolism in adulthood. Yet, whether KCs influence neonatal hepatocyte metabolism is unknown. Here, using conditional knockout mouse models targeting macrophages, we demonstrate that yolk sac-derived KCs play a critical role in hepatocyte glycogen storage and function by regulating the TCA cycle - a role that monocyte-derived KC-like cells cannot substitute. in order to check the lipid levels after birth, Newborn pups were collected and the different lipid species were assessd by lipidomics analysis using mass spectrometer.
Institute	University of Bonn
Department	Developmental Biology of the Immune System, The Life & Medical Sciences Institute (LIMES)
Laboratory	Mass Lab
Last Name	Makdissi
First Name	Nikola
Address	Carl Troll straße 31, Bonn
Email	nmakdissi@uni-bonn.de
Phone	02 28 / 73 - 6 2794
Submit Date	2024-11-07
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-02-11
Release Version	1

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Project:

Project ID:	PR002234
Project DOI:	doi: 10.21228/M8VJ9K
Project Title:	Kupffer cells control neonatal hepatic glucose metabolism via Igf1 signaling
Project Type:	lipidomics analysis
Project Summary:	During perinatal development, liver metabolism is tightly regulated to ensure energy supply for the newborn. Before birth, glycogen is stored in hepatocytes and later metabolized to glucose, meeting the energy demands of the neonate. Shortly after birth, lipogenesis begins, driven by the transcriptional activation of enzymes involved in fatty acid oxidation. These processes are thought to be largely regulated by systemic insulin and glucagon levels. However, the role of liver-derived local factors in neonatal hepatocyte metabolism remains unexplored. Kupffer cells (KCs), the liver’s resident macrophages, colonize the fetal liver early in embryogenesis and support liver metabolism in adulthood. Yet, whether KCs influence neonatal hepatocyte metabolism is unknown. Here, using conditional knockout mouse models targeting macrophages, we demonstrate that yolk sac-derived KCs play a critical role in hepatocyte glycogen storage and function by regulating the TCA cycle - a role that monocyte-derived KC-like cells cannot substitute. Newborn pups lacking KCs mobilize glycogen more rapidly, a process regulated by insulin-like growth factor 1 (Igf1) production. Our findings reveal that macrophages are a major source of Igf1 at birth and that local Igf1 production by KCs is essential for balanced hepatocyte metabolism.
Institute:	University of Bonn
Department:	Developmental Biology of the Immune System, The Life & Medical Sciences Institute (LIMES)
Laboratory:	Mass Lab
Last Name:	Makdissi
First Name:	Nikola
Address:	Carl Troll straße 31, Bonn
Email:	nmakdissi@uni-bonn.de
Phone:	02 28 / 73 - 6 2794

Subject:

Subject ID:	SU003743
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Age Or Age Range:	postnatal day 0

Factors:

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

mb_sample_id	local_sample_id	genotypes
SA392814	ko_2_pos	KO
SA392815	ko_4_pos	KO
SA392816	ko_5_pos	KO
SA392817	ko_7_pos	KO
SA392818	ko_9_pos	KO
SA392819	wt_1_pos	WT
SA392820	wt_3_pos	WT
SA392821	wt_6_pos	WT
SA392822	wt_8_pos	WT
SA392823	wt_10_pos	WT

Showing results 1 to 10 of 10

Showing results 1 to 10 of 10

Collection:

Collection ID:	CO003736
Collection Summary:	The livers of P0 pups were collected in cold PBS then snap frozen in Nitrogen.
Sample Type:	Liver
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR003752
Treatment Summary:	No treatment. P0 livers from the Spiflox Tnfrsf11aeGFPCre mouse model were snap frozen in Nitrogen. The pups were WT(Spif/f Tnfrsf11aeGFP+/+) and KO (Spif/f Tnfrsf11aeGFPCre/+)

Sample Preparation:

Sampleprep ID:	SP003750
Sampleprep Summary:	Lipid extraction and tandem mass spectrometry: To evaluate differences in hepatic lipid metabolism tandem mass spectrometry of extracted lipids was performed. For this purpose, 10 mg liver tissue was homogenized in 500 μL ddH2O on ice. Then, 50 μL of the homogenate was transferred into a fresh Eppendorf tube and 500 μL Extraction Mix (CHCl3/MeOH 1/5 containing the following internal standards: 210 pmol PE(31:1), 396 pmol PC(31:1), 98 pmol PS(31:1), 84 pmol PI(34:0), 56 pmol PA(31:1), 51 pmol PG (28:0), 28 pmol CL(56:0), 39 pmol LPA (17:0), 35 pmol LPC(17:1), 38 pmol LPE (17:0), 32 pmol Cer(17:0), 99 pmol, SM(17:0), 55 pmol GlcCer(12:0), 14 pmol GM3 (18:0-D3), 339 pmol TG(50:1-d4), 111 pmol, CE(17:1), 64 pmol DG(31:1), 103 pmol MG(17:1), 724 pmol Chol(d6) and 45 pmol Car(15:0) was added. After 2 min of sonication in a bath sonicator, the samples were spun at 20,000 g for 2 min. The supernatant was collected in a new Eppendorf tube and 200 μL chloroform and 750 μL of 1 M Ammonium acetate (NH4Ac) in ddH2O were added. Following quick manual shaking, the samples were centrifuged at 20,000 g for 2 min again. The upper phase was carefully removed, and the lower phase was transferred into a new Eppendorf tube. The solvent was evaporated using a SpeedVac Vacuum Concentrator at 45 °C for 20 min. The dried lipids were dissolved in 500 μL Spray Buffer (Isopropanol, Methanol, ddH2O (all MS grade), 10 mM ammonium acetate, 0.1 % acetic acid by sonication for 5 min. Until measurement with a Thermo Q Exactive ™ Plus (Thermo Scientific) using positive mode, the samples were stored at -20 °C. Before the acquisition, the samples were sonicated for 5 min.

Sampleprep ID:

SP003750

Sampleprep Summary:

Lipid extraction and tandem mass spectrometry: To evaluate differences in hepatic lipid metabolism tandem mass spectrometry of extracted lipids was performed. For this purpose, 10 mg liver tissue was homogenized in 500 μL ddH2O on ice. Then, 50 μL of the homogenate was transferred into a fresh Eppendorf tube and 500 μL Extraction Mix (CHCl3/MeOH 1/5 containing the following internal standards: 210 pmol PE(31:1), 396 pmol PC(31:1), 98 pmol PS(31:1), 84 pmol PI(34:0), 56 pmol PA(31:1), 51 pmol PG (28:0), 28 pmol CL(56:0), 39 pmol LPA (17:0), 35 pmol LPC(17:1), 38 pmol LPE (17:0), 32 pmol Cer(17:0), 99 pmol, SM(17:0), 55 pmol GlcCer(12:0), 14 pmol GM3 (18:0-D3), 339 pmol TG(50:1-d4), 111 pmol, CE(17:1), 64 pmol DG(31:1), 103 pmol MG(17:1), 724 pmol Chol(d6) and 45 pmol Car(15:0) was added. After 2 min of sonication in a bath sonicator, the samples were spun at 20,000 g for 2 min. The supernatant was collected in a new Eppendorf tube and 200 μL chloroform and 750 μL of 1 M Ammonium acetate (NH4Ac) in ddH2O were added. Following quick manual shaking, the samples were centrifuged at 20,000 g for 2 min again. The upper phase was carefully removed, and the lower phase was transferred into a new Eppendorf tube. The solvent was evaporated using a SpeedVac Vacuum Concentrator at 45 °C for 20 min. The dried lipids were dissolved in 500 μL Spray Buffer (Isopropanol, Methanol, ddH2O (all MS grade), 10 mM ammonium acetate, 0.1 % acetic acid by sonication for 5 min. Until measurement with a Thermo Q Exactive ™ Plus (Thermo Scientific) using positive mode, the samples were stored at -20 °C. Before the acquisition, the samples were sonicated for 5 min.

Combined analysis:

Analysis ID	AN005939
Chromatography ID	CH004514
MS ID	MS005656
Analysis type	MS
Chromatography type	None (Direct infusion)
Chromatography system	none
Column	none
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive Plus Orbitrap
Ion Mode	POSITIVE
Units	pmol/g tissue

Chromatography:

Chromatography ID:	CH004514
Instrument Name:	none
Column Name:	none
Column Temperature:	none
Flow Gradient:	none
Flow Rate:	none
Solvent A:	none
Solvent B:	none
Chromatography Type:	None (Direct infusion)

MS:

MS ID:	MS005656
Analysis ID:	AN005939
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The samples were run on the positive mode and the raw data were processed using LipidXplorer. Analysed data was taken relative to the internal standerd for each species and then the lipid abundance was calculated per gram of tissue. NOTE: "0" values indicate that the metabolite wasn't detected, while the "NA" indicates that the metabolite was detected but wasn't able to be calculated because the internal standard wasn't detected in the individual sample.
Ion Mode:	POSITIVE