Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential gene expression in the brainstem of uninfected and West Nile Virus infected C57BL6/J and Sarm1-em3AGS mice

ABSTRACT: The Toll/IL-1R domain-containing adaptor protein SARM1 is expressed primarily in the brain, where it mediates axonal degeneration. Additional roles for SARM1 in a number of other processes including TLR-signaling, viral infection, chemokine expression, and XAF1 expression have also been described. Here we report defects in the induction of Ccl3, Ccl4, and Ccl5 in Sarm1-/- macrophages, for which we were unable to find mechanistic support. We instead show that the 129 congenic locus spans both the chemokine and XAF1 loci, and SNP analysis reveals other remaining 129 genomic regions in both existing knockout strains. New knockout mouse strains generated on a pure B6 genetic background using CRISPR confirmed the role of SARM1 in axonal degeneration and susceptibility WNV infection, but not in chemokine expression or susceptibility to VSV or LACV infection. We show that XAF1 expression differences are due to sequence and isoform polymorphism between B6 and 129 strains. Given its known role in apoptosis, XAF1 polymorphism may account for some phenotypes described in Sarm1-/- mice. RNAseq in the new CRISPR strains reveals changes in transcripts of the mitochondrial electron transport chain and ribosomal proteins, suggesting possible targets of SARM1.

ORGANISM(S): Mus musculus

PROVIDER: GSE136221 | GEO | 2020/02/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

RNAseq of C57BL/6J and C57BL6/J Sarm1-deficient mice to determine if genes surrounding the knockout locus are B6 or 129 sequence

Project description:The Toll/IL-1R domain-containing adaptor protein SARM1 is expressed primarily in the brain, where it mediates axonal degeneration. Additional roles for SARM1 in a number of other processes including TLR-signaling, viral infection, chemokine expression, and XAF1 expression have also been described. Here we report defects in the induction of Ccl3, Ccl4, and Ccl5 in Sarm1-/- macrophages, for which we were unable to find mechanistic support. We instead show that the 129 congenic locus spans both the chemokine and XAF1 loci, and SNP analysis reveals other remaining 129 genomic regions in both existing knockout strains. New knockout mouse strains generated on a pure B6 genetic background using CRISPR confirmed the role of SARM1 in axonal degeneration and susceptibility WNV infection, but not in chemokine expression or susceptibility to VSV or LACV infection. We show that XAF1 expression differences are due to sequence and isoform polymorphism between B6 and 129 strains. Given its known role in apoptosis, XAF1 polymorphism may account for some phenotypes described in Sarm1-/- mice. RNAseq in the new CRISPR strains reveals changes in transcripts of the mitochondrial electron transport chain and ribosomal proteins, suggesting possible targets of SARM1.

2020-02-23 | GSE136284 | GEO

A Conformation specific Nanobody Targeting the NMN-activated State of SARM1

Project description:Upon axonal injury, Sterile alpha (SAM) and Toll/interleukin-1 receptor (TIR) motif containing 1 (SARM1) is activated by nicotinamide mononucleotide (NMN) to deplete NAD and consequently promote the process of axon degeneration (AxD). Currently, only the inactive form of SARM1 in its auto-inhibitory conformation has been resolved. The flexibility of the enzymatically active form of SARM1 has so far precluded its structural determination. To solve the problem, we generated a stabilizing nanobody, Nb-C6, that specifically recognized 30 only the NMN-activated form of SARM1. The conformation specificity was verified by immunoprecipitation and surface plasmon resonance. Fluorescently labeled Nb-C6 could immunostain only the activated SARM1 in cells stimulated with CZ-48, a permeant mimetic of NMN. Expression of Nb-C6 in live cells resulted in stabilization of the active form of the endogenous and exogenous SARM1, producing and elevating cellular levels of cyclic ADP-ribose, a calcium messenger. Cryo-EM of the NMN-activated SARM1 complexed by Nb-C6 showed an octameric structure resembling a “blooming lotus” with the ARM domains bending significantly inward and swinging out together with the TIR domains to form the “petals of the lotus”. Nb-C6 bound to the SAM domain of the activated SARM1 and stabilized its Armadillo repeat motif domain. Analyses using hydrogen-deuterium exchange mass spectrometry (HDX-MS), and cross-linking MS (XL-MS) indicate that the activated SARM1 is highly dynamic and flexible and the neighboring TIRs form dimers via the surface close to one BB loop. The Nanobody is thus a valuable tool for delineating the mechanism of activation of SARM1 in AxD and other cellular processes.

2022-11-29 | PXD033528 | Pride

Selective inhibitors of SARM1 targeting an allosteric cysteine in the autoregulatory ARM domain

Project description:The NAD hydrolase (NADase) SARM1 acts as a central executioner of programmed axon death and is a possible therapeutic target for neurodegenerative disorders. While orthosteric inhibitors of SARM1 have been described, this multi-domain enzyme is also subject to intricate forms of autoregulation, suggesting the potential for allosteric modes of inhibition. Previous studies have identified multiple cysteine residues that support SARM1 activation and catalysis, but which of these cysteines, if any, might be selectively targetable by electrophilic small molecules remains unknown. Here we describe the chemical proteomic discovery of a series of tryptoline acrylamides that site-specifically and stereoselectively modify cysteine-311 (C311) in the non-catalytic, autoregulatory armadillo repeat (ARM) domain of SARM1. These covalent compounds inhibit the NADase activity of WT-SARM1, but not C311A or C311S SARM1 mutants, show a high degree of proteome-wide selectivity for SARM1_C311, and stereoselectively block vincristine- and vacor-induced neurite degeneration in primary rodent dorsal root ganglion neurons. Our findings describe selective, covalent inhibitors of SARM1 targeting an allosteric cysteine, pointing to a potentially attractive therapeutic strategy for axon degeneration-dependent forms of neurological disease.

2022-08-22 | PXD035400 | Pride

mRNA-seq of wild-type or XAF1 knockout HT29 cells after vesicular stomatitis virus infection

Project description:To investigate the function of XAF1 in immune response, we established XAF1 knockout cell lines in which XAF1 gene has been knockout by sgRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of WT or XAF1 knockout HT29 cells with or without VSV infection

2023-01-01 | GSE220273 | GEO

NFIA determines the cis-effect of genetic variation on adipocyte browning in mice [WGS]

Project description:Thermogenic brown and beige adipocytes counteract obesity by enhancing energy dissipation via uncoupling proein-1 (Ucp1). However, the effect of genetic variation on these cells, a major source of disease susceptibility, has been less well studied. Here we examined beige adipocytes from obesity-prone C57BL/6J (B6) and obesity-resistant 129X1/SvJ (129) mouse strains and identified a cis-regulatory variant rs47238345 that is responsible for differential Ucp1 expression. The alternative T allele of rs47238345 at the Ucp1 -12kb enhancer in 129 facilitates the allele-specific binding of nuclear factor I-A (NFIA) to mediate allele-specific enhancer-promoter interaction and Ucp1 transcription. We also identified Lim homeobox protein 8 (Lhx8), whose expression is higher in 129 than in B6, as a trans-acting regulator of Ucp1 in mice and humans. These results demonstrate the cis- and trans-acting effects of genetic variation on Ucp1 expression that underlie phenotypic diversity.

2022-07-27 | GSE188261 | GEO

NFIA determines the cis-effect of genetic variation on adipocyte browning in mice [HiC]

2022-07-27 | GSE188260 | GEO

NFIA determines the cis-effect of genetic variation on adipocyte browning in mice [ChIP-Seq]

2022-07-27 | GSE186904 | GEO

NFIA determines the cis-effect of genetic variation on adipocyte browning in mice [RNA-Seq]

2022-07-27 | GSE186903 | GEO

Sarm1 knockout prevents type 1 diabetic bone disease in females independent of neuropathy

Project description:Diabetic patients have a high risk of developing skeletal diseases accompanied by diabetic peripheral neuropathy (DPN). In this study, we isolated the role of DPN in skeletal disease with global and conditional knockout models of sterile-α and TIR-motif-containing protein-1 (Sarm1). SARM1, an NADase highly expressed in the nervous system, regulates axon degeneration upon a range of insults, including DPN. Global knockout of Sarm1 prevented DPN, but not skeletal disease, in male mice with type 1 diabetes (T1D). Female wild type mice also developed diabetic bone disease, but without DPN. Unexpectedly, global Sarm1 knockout completely protected female mice from T1D-associated bone suppression and skeletal fragility despite comparable muscle atrophy and hyperglycemia. Global Sarm1 knockout rescued bone health through sustained osteoblast function with abrogation of local oxidative stress responses. This was independent of the neural actions of SARM1, as beneficial effects on bone were lost with neural conditional Sarm1 knockout. This study demonstrates that the onset of skeletal disease occurs rapidly in both male and female mice with T1D completely independent of DPN. In addition, this reveals that clinical SARM1 inhibitors, currently being developed for treatment of neuropathy, may also have benefits for diabetic bone through actions outside of the nervous system.

2024-04-30 | GSE252292 | GEO

Macrophage depletion blocks congenital SARM1-dependent neuropathy

Project description:Axon loss contributes to many common neurodegenerative disorders. In healthy axons, the axon survival factor NMNAT2 inhibits SARM1, the central executioner of programmed axon degeneration. We identified two rare NMNAT2 missense variants in two brothers afflicted with a progressive neuropathy syndrome. The polymorphisms result in amino acid substitutions, V98M and R232Q, which reduce NMNAT2 NAD+-synthetase activity. We generated a mouse model of the human syndrome and found that Nmnat2V98M/Nmnat2R232Q compound-heterozygous CRISPR mice survive to adulthood but develop progressive motor dysfunction, peripheral axon loss, and macrophage infiltration. These disease phenotypes are all SARM1-dependent. Remarkably, macrophage depletion therapy blocks and reverses neuropathic phenotypes in Nmnat2V98M/R232Q mice, identifying a SARM1-dependent neuroimmune mechanism as a key driver of disease pathogenesis. These findings demonstrate that SARM1 induces an inflammatory neuropathy and highlight the potential of immune therapy to treat this rare syndrome and other neurodegenerative conditions associated with NMNAT2 loss and SARM1 activation.

2022-10-25 | GSE210403 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data