GSM2876265: iR2ko_355; Mus musculus; RNA-Seq - SRA

SRX3445305: GSM2876265: iR2ko_355; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 46.6M spots, 2.4G bases, 1.5Gb downloads

Submitted by: NCBI (GEO)

Study: iRhom2 Promotes Lupus Nephritis through ADAM17-Dependent TNF-a and EGFR Signaling

PRJNA421160 • SRP126164 • All experiments • All runs

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Lupus nephritis (LN) often results in progressive renal dysfunction. The inactive Rhomboid 2 (iRhom2) is a newly identified key regulator of A disintegrin and metalloprotease 17 (ADAM17), whose substrates, such as TNF-a and heparin-binding EGF (HB-EGF), have been implicated in the pathogenesis of chronic kidney disease. Here we demonstrate that deficiency of iRhom2 protects the lupus-prone Fcgr2b-/- mice from developing severe kidney damage without altering anti-double stranded (ds) DNA Ab production, by simultaneously blocking the HB-EGF/EGFR and the TNF-a signaling in the kidney tissues. Unbiased transcriptome profiling of kidneys and kidney macrophages revealed that TNF-a and HB-EGF/EGFR signaling pathways are highly upregulated in Fcgr2b-/- mice; alterations that were diminished in the absence of iRhom2. Pharmacological blockade of either TNF-a or EGFR signaling protected Fcgr2b-/- mice from severe renal damage. Finally, kidneys from LN patients showed increased iRhom2 and HB-EGF expression, with interstitial HB-EGF expression significantly associated with chronicity indices. Our data suggest that activation of iRhom2/ADAM17-dependent TNF-a and EGFR signaling plays a crucial role in mediating irreversible kidney damage in LN, thereby uncovering a novel target for selective and simultaneous dual inhibition of two major pathological pathways in the effector arm of the disease. Overall design: [1] Analysis of total kidney transcriptomes in Fcgr2b-/- mice, Rhbdf2-/- mice; Rhbdf2 -/- Fcgr2b-/- mice and the wildtype control. [2] Analysis of CD45+F4/80hiCD11b+Ly6G-Ly6C- kidney macrophages transcriptomes in Fcgr2b-/- mice, Rhbdf2-/- mice; Rhbdf2 -/- Fcgr2b-/- mice and the wildtype control.

Sample: iR2ko_355

SAMN08133519 • SRS2735719 • All experiments • All runs

Organism: Mus musculus

Library:

Instrument: Illumina HiSeq 2500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Construction protocol: 1. For RNA-sequencing in whole kidneys, total RNA was extracted from whole kidneys from well-perfused mice using an RNeasy mini kit (Qiagen). 2. For sorted macrophages, kidneys from 7-9 m old mice were first minced and digested with collagenase B (Roche) for 45 minutes at 37ºC. Macrophages were enriched by centrifuging cells in 40% percoll/PBS (v/v). Cells were stained with fluorochrome-conjugated anti-mouse antibodies, and CD45+F4/80hiCD11b+Ly6G-Ly6C- kidney macrophages were sorted into RLT lysis buffer directly. Total RNA was extracted using an RNeasy mini kit (Qiagen). 1. For total kidney, library preparation and sequencing were performed by Genomics Resources Core Facility at Weill Cornell Medical College using TruSeq RNA library prep kit (Illumina) followed by single read sequencing on the Illumina HiSeq 2500 instrument (4-6 samples/SR lane, 50 bp reads). 2. For sorted macrophages, library preparation and sequencing were performed at Epigenetics Core facility at Weill Cornell Medical College using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) followed by single read clustering and 51 cycles sequencing on the Illumina HiSeq 2500 instrument.

Experiment attributes:

GEO Accession: GSM2876265

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 46.6M spots, 2.4G bases, 1.5Gb

Run	# of Spots	# of Bases	Size	Published
SRR6348219	46,559,785	2.4G	1.5Gb	2019-01-02

ID:: 4802752

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