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Series GSE135788

Query DataSets for GSE135788

Status

Public on Aug 14, 2019

Title

Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche (microarray)

Organism

Experiment type

Expression profiling by array
Third-party reanalysis

Summary

Macrophages are strongly adapted to their tissue of residence. Yet, we know little about the cell-cell interactions that imprint the tissue-specific identities of macrophages in their respective niches. Using conditional depletion of liver Kupffer cells, we traced the developmental stages of monocytes differentiating into Kupffer cells and mapped the cellular interactions imprinting the Kupffer cell identity. Kupffer cell loss induced the tumor necrosis factor (TNF) and interleukin-1 (IL-1) receptor-dependent activation of stellate cells and endothelial cells, resulting in the transient production of chemokines and adhesion molecules orchestrating monocyte engraftment. Engrafted circulating monocytes transmigrated into the perisinusoidal space, and acquired the liver-associated transcription factors ID3 and LXRα. Coordinated interactions with hepatocytes induced ID3 expression, while endothelial cells and stellate cells induced LXRα via a synergistic NOTCH-BMP pathway. This study shows that the Kupffer cell niche is composed of stellate cells, hepatocytes and endothelial cells that together imprint the liver-specific macrophage identity.

Overall design

Microarray = different time points during development of Kupffer cells during embryogenesis and after depletion. This data was compared to previously published data (GSE76999, GSE75225 and GSE117080) and to other tissue resident macrophages from the Immgen Consortium Database (GSE15907).
Bulk RNA Seq = Hepatic Stellate Cells (HSCs), Liver Sinusoidal Endothelial Cells (LSECs) and hepatocytes. For each cell type there are 4 replicates from Pbs mice, 12h after DT-injection mice and 36h after DT-injection mice.

Contributor(s)

Bonnardel J, T’Jonck W, Gaublomme D, Browaeys R, Scott CL, Martens L, Vanneste B, De Prijck S, Nedospasov S, Kremer A, Van Hamme E, Borghgraef P, Toussaint W, De Bleser P, Mannaerts I, Beschin A, van Grunsven L, Lambrecht BN, Taghon T, Lippens S, Elewaut D, Saeys Y, Guilliams M

Citation(s)

Submission date

Aug 13, 2019

Last update date

Dec 09, 2019

Contact name

Liesbet Martens

E-mail(s)

liesbet.martens@irc.vib-ugent.be

Organization name

VIB-University of Ghent

Department

VIB Inflammation Research Center

Street address

Technologiepark 927

City

Zwijnaarde

ZIP/Postal code

9052

Country

Belgium

Platforms (1)

[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]

Samples (36)

More...

GSM4030124	Monocytes 1 day after Kupffer cell depletion mono_D1_1
GSM4030125	Monocytes 1 day after Kupffer cell depletion mono_D1_2
GSM4030126	Monocytes 1 day after Kupffer cell depletion mono_D1_3

GSM4030127	F4/80+ macrophages 3 days after Kupffer cell depletion F4-80pos_mac_D3_1
GSM4030128	F4/80+ macrophages 3 days after Kupffer cell depletion F4-80pos_mac_D3_1.1
GSM4030129	F4/80+ macrophages 3 days after Kupffer cell depletion F4-80pos_mac_D3_1.2
GSM4030130	Clec4f+ macrophages 7 days after Kupffer cell depletion C4pos_mac_D7_1
GSM4030131	Clec4f+ macrophages 7 days after Kupffer cell depletion C4pos_mac_D7_2
GSM4030132	Clec4f+ macrophages 7 days after Kupffer cell depletion C4pos_mac_D7_3
GSM4030133	Yolk sac macrophages at day 11 of embryogenesis yolkSac_mac_E11_1
GSM4030134	Yolk sac macrophages at day 11 of embryogenesis yolkSac_mac_E11_2
GSM4030135	Yolk sac macrophages at day 11 of embryogenesis yolkSac_mac_E11_3
GSM4030136	Clec4f- macrophages at day 12 of embryogenesis C4neg_mac_E12_1
GSM4030137	Clec4f- macrophages at day 12 of embryogenesis C4neg_mac_E12_2
GSM4030138	Clec4f- macrophages at day 12 of embryogenesis C4neg_mac_E12_3
GSM4030139	Clec4f- macrophages at day 12 of embryogenesis C4neg_mac_E12_4
GSM4030140	Clec4f- macrophages at day 15 of embryogenesis C4neg_mac_E15_1
GSM4030141	Clec4f- macrophages at day 15 of embryogenesis C4neg_mac_E15_2
GSM4030142	Clec4f- macrophages at day 15 of embryogenesis C4neg_mac_E15_3
GSM4030143	Clec4f- macrophages at day 15 of embryogenesis C4neg_mac_E15_4
GSM4030144	Clec4f- macrophages at day 17 of embryogenesis C4neg_mac_E17_1
GSM4030145	Clec4f- macrophages at day 17 of embryogenesis C4neg_mac_E17_2
GSM4030146	Clec4f- macrophages at day 17 of embryogenesis C4neg_mac_E17_3
GSM4030147	Clec4f- macrophages at day 17 of embryogenesis C4neg_mac_E17_4
GSM4030148	Clec4f+ macrophages at day 17 of embryogenesis C4pos_mac_E17_1
GSM4030149	Clec4f+ macrophages at day 17 of embryogenesis C4pos_mac_E17_2
GSM4030150	Clec4f+ macrophages at day 17 of embryogenesis C4pos_mac_E17_3
GSM4030151	Clec4f+ macrophages at day 17 of embryogenesis C4pos_mac_E17_4
GSM4030152	Clec4f+ macrophages at day 18 of embryogenesis C4pos_mac_E18_1
GSM4030153	Clec4f+ macrophages at day 18 of embryogenesis C4pos_mac_E18_2
GSM4030154	Clec4f+ macrophages at day 18 of embryogenesis C4pos_mac_E18_3
GSM4030155	Clec4f+ macrophages at day 18 of embryogenesis C4pos_mac_E18_4
GSM4030156	Kupffer cells at day of birth KC_D0_1
GSM4030157	Kupffer cells at day of birth KC_D0_2
GSM4030158	Kupffer cells at day of birth KC_D0_3
GSM4030159	Kupffer cells at day of birth KC_D0_4

This SubSeries is part of SuperSeries:

Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche

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BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE135788_81_samples_RMA.txt.gz	15.0 Mb	(ftp)(http)	TXT
GSE135788_RAW.tar	144.8 Mb	(http)(custom)	TAR (of CEL)
Processed data included within Sample table
Processed data are available on Series record

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