Summary of Study ST003702

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	ST003702
Study Title	Kupffer cells control neonatal hepatic glucose metabolism via Igf1 signaling - lipidomics analysis of postnatal day 0 murine livers after macrophages depletion using Csf1r conditional KO
Study Type	lipidomics analysis of P0 livers from mice after macrophages depletion by Csf1r conditional KO
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 (Csf1r-flox Tnfrsf11a-Cre), 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
Email	nmakdissi@uni-bonn.de
Phone	02 28 / 73 - 6 2794
Submit Date	2025-01-15
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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Sample Preparation:

Sampleprep ID:	SP003840
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:

SP003840

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.