Summary of Study ST002177

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 PR001385. The data can be accessed directly via it's Project DOI: 10.21228/M8PT3H 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.

Show all samples | Perform analysis on untargeted data
Download mwTab file (text) | Download mwTab file(JSON) | Download data files (Contains raw data)

Study ID	ST002177
Study Title	Multiomics Analyses Reveal the Central Role of Pentose Phosphate Pathway in Resident Thymic Macrophages to Cope with Efferocytosis-Associated Stress
Study Summary	Tissue-resident macrophages (TRMs) are heterogeneous cell populations found throughout the body. Depending on their location, they perform diverse functions maintaining tissue homeostasis and providing immune surveillance. To survive and function within, TRMs adapt metabolically to the distinct microenvironments. However, little is known about the metabolic signatures of TRMs. The thymus provides a nurturing milieu for developing thymocytes yet efficiently removes those that failed the selection, relying on the TRMs – resident thymic macrophages (TMφs). This study harnesses multiomics analyses to characterize TMφs and unveils their unique metabolic features. We find that the pentose phosphate pathway (PPP) is preferentially activated in TMφs, responding to the reduction-oxidation demands associated with the efferocytosis of dying thymocytes. The blockade of PPP in Mφs leads to decreased efferocytosis, which can be rescued by ROS scavengers. Our study reveals the key role of PPP in TMφs and underscores the importance of metabolic adaptation in supporting Mφ efferocytosis.
Institute	National Yang Ming Chiao Tung University
Department	Institute of Microbiology and Immunology
Laboratory	Chai-Lin Hsu
Last Name	Hsu
First Name	Chia-Lin
Address	R309, Biomedical Building, NYCU, No. 155, Sec. 2, Linong St., Beitou Dist. Taipei 112, Taiwan
Email	clhsu@nycu.edu.tw
Phone	+886-2-2826-7000 ext:65619
Submit Date	2022-05-21
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2022-06-09
Release Version	1

Select appropriate tab below to view additional metadata details:

Treatment:

Treatment ID:	TR002275
Treatment Summary:	To obtain the resident thymic macrophages, the thymus was harvested from 5 to 8 weeks old C57BL mice, cut into small pieces, and incubated in DMEM containing 0.4 mg/mL collagenase P and 0.4 mg/mL DNase I at 37˚C for 20 min with frequent gentle mixing. The resulting cell suspension was overlaid on the 57% Percoll Plus solution at the volume ratio of 1:1 and centrifuged at 650 x g for 20 min at 4˚C. The cells at the interface were collected and washed with PBS, and re-suspended in 24G2 supernatant at room temperature for 15 min for blocking. The anti-CD64, anti-CD11b, and anti-F4/80 antibody cocktail in FACS buffer (PBS with 0.5% bovine serum albumin (BSA) and 2 mM EDTA) was added to the sample and allowed incubation on ice for 20 min. At the end of the staining, the cells were centrifuged, washed, and re-suspended in propidium iodide containing FACS buffer. Live singlets with CD64+CD11bloF4/80+ were defined as resident thymic macrophages (TMφs) and sorted by BD FACSMelody with the purity > 95%. The peritoneal cavity macrophages (PCMφs) were collected by intra-peritoneal injected 5 mL of ice-cold complete DMEM, thoroughly rinsed the peritoneal cavity, and re-collected the solution containing the exudate cells. The cells were processed and stained as described above, and the CD11b+F4/80+ cells were identified as PCMφs and harvested.

Treatment ID:

TR002275

Treatment Summary:

To obtain the resident thymic macrophages, the thymus was harvested from 5 to 8 weeks old C57BL mice, cut into small pieces, and incubated in DMEM containing 0.4 mg/mL collagenase P and 0.4 mg/mL DNase I at 37˚C for 20 min with frequent gentle mixing. The resulting cell suspension was overlaid on the 57% Percoll Plus solution at the volume ratio of 1:1 and centrifuged at 650 x g for 20 min at 4˚C. The cells at the interface were collected and washed with PBS, and re-suspended in 24G2 supernatant at room temperature for 15 min for blocking. The anti-CD64, anti-CD11b, and anti-F4/80 antibody cocktail in FACS buffer (PBS with 0.5% bovine serum albumin (BSA) and 2 mM EDTA) was added to the sample and allowed incubation on ice for 20 min. At the end of the staining, the cells were centrifuged, washed, and re-suspended in propidium iodide containing FACS buffer. Live singlets with CD64+CD11bloF4/80+ were defined as resident thymic macrophages (TMφs) and sorted by BD FACSMelody with the purity > 95%. The peritoneal cavity macrophages (PCMφs) were collected by intra-peritoneal injected 5 mL of ice-cold complete DMEM, thoroughly rinsed the peritoneal cavity, and re-collected the solution containing the exudate cells. The cells were processed and stained as described above, and the CD11b+F4/80+ cells were identified as PCMφs and harvested.