Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Emc1_Marquez - Disrupted ER membrane protein complex-mediated topogenesis drives congenital neural crest defects

ABSTRACT: Experiment consisted of MO knockdown of emc1 in Xenopus and comparison of proteome in emc1 depleted stage 24 embryos vs MO control injected embryos.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Xenopus Tropicalis

TISSUE(S): Whole Body, Early Embryonic Cell

DISEASE(S): Congenital Heart Disease

SUBMITTER: Jonathan Marquez

LAB HEAD: Mustafa K Khokha

PROVIDER: PXD012770 | Pride | 2020-01-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	LF18-020_Marquez_Khokha_rnk10_iso2_F508894_PRIDE_export.MSMS.mgf	Mgf
	LF18-020_Marquez_Khokha_rnk10_iso2_F508894_PRIDE_export.MSMS.pride.mgf.gz	Mgf
	LF18-020_Marquez_Khokha_rnk10_iso2_F508894_PRIDE_export.mzid.gz	Mzid
	LF18-020_Marquez_Khokha_rnk10_iso2_F508894_PRIDE_export.pride.mztab.gz	Mztab
	QEp18-1014_Khokha_Control_1.raw	Raw

Items per page:

1 - 5 of 10

Publications

Disrupted ER membrane protein complex-mediated topogenesis drives congenital neural crest defects.

Marquez Jonathan J Criscione June J Charney Rebekah M RM Prasad Maneeshi S MS Hwang Woong Y WY Mis Emily K EK García-Castro Martín I MI Khokha Mustafa K MK

The Journal of clinical investigation 20200201 2

Multipass membrane proteins have a myriad of functions, including transduction of cell-cell signals, ion transport, and photoreception. Insertion of these proteins into the membrane depends on the endoplasmic reticulum (ER) membrane protein complex (EMC). Recently, birth defects have been observed in patients with variants in the gene encoding a member of this complex, EMC1. Patient phenotypes include congenital heart disease, craniofacial malformations, and neurodevelopmental disease. However, ...[more]

PMID: 31904590

Similar Datasets

Disrupted ER membrane protein complex-mediated topogenesis drives congenital neural crest defects.

Project description:Multipass membrane proteins have a myriad of functions, including transduction of cell-cell signals, ion transport, and photoreception. Insertion of these proteins into the membrane depends on the endoplasmic reticulum (ER) membrane protein complex (EMC). Recently, birth defects have been observed in patients with variants in the gene encoding a member of this complex, EMC1. Patient phenotypes include congenital heart disease, craniofacial malformations, and neurodevelopmental disease. However, a molecular connection between EMC1 and these birth defects is lacking. Using Xenopus, we identified defects in neural crest cells (NCCs) upon emc1 depletion. We then used unbiased proteomics and discovered a critical role for emc1 in WNT signaling. Consistent with this, readouts of WNT signaling and Frizzled (Fzd) levels were reduced in emc1-depleted embryos, while NCC defects could be rescued with β-catenin. Interestingly, other transmembrane proteins were mislocalized upon emc1 depletion, providing insight into additional patient phenotypes. To translate our findings back to humans, we found that EMC1 was necessary for human NCC development in vitro. Finally, we tested patient variants in our Xenopus model and found the majority to be loss-of-function alleles. Our findings define molecular mechanisms whereby EMC1 dysfunction causes disease phenotypes through dysfunctional multipass membrane protein topogenesis.

| S-EPMC6994125 | biostudies-literature

Transcription profiling of Xenopus embryonic posterior mesoderm controls and Derriere depleted embryos

Project description:Left-right axis determination is a fundamental and conserved developmental process, with consequences for human pathology. At the molecular level, this process requires at least two centers of nodal-type TGFbeta signals: the first center, containing nodal/Xn; Microarrays were used to determine differences in gene expression in posterior mesoderm of Xenopus embryos. We compared controls and Derriere depleted embryos. Experiment Overall Design: Microarrays were used to determine differences in gene expression in posterior mesoderm of Xenopus embryos. We compared controls and embryos depleted of Derriere protein using MO oligonucleotides.

2009-02-09 | E-GEOD-13882 | biostudies-arrayexpress

Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus

Project description:We report on the implications of genetic KO versus MO-mediated KD of the mesoderm-specifying Brachyury paralogues in the Western clawed frog Xenopus tropicalis. While both KO and KD embryos fail to activate the same core gene regulatory network, resulting in virtually identical morphological defects, embryos injected with control or target MOs also show a systemic GC content dependent immune response and many off-target splicing defects.

2018-02-21 | GSE96655 | GEO

Transcription profiling of Xenopus embryos

Project description:Xenopus laevis embryos were injected with mRNA for EFTFs at 2-cell stage. Animal caps collected at stage 9, cultured to the equivalent of stage 15 and RNA extracted. Four biological replicates of the EFTF-injected and GFP-injected (control) caps were used to profile transcript expression patterns using Affymetrix Xenopus Laevis GeneChip microarrays. Experiment Overall Design: Xenopus laevis embryos were injected with mRNA for EFTFs at 2-cell stage. Animal caps collected at stage 9, cultured to the equivalent of stage 15 and RNA extracted. Four biological replicates of the EFTF-injected and GFP-injected (control) caps were used to profile transcript expression patterns using Affymetrix Xenopus Laevis GeneChip microarrays.

2009-09-15 | E-GEOD-9173 | biostudies-arrayexpress

Transcription profiling of Xenopus eye primordia vs. posterior neural plate vs. lateral endoderm normalized the whole embryos

Project description:Tissues from the eye primordia, lateral endoderm, and posterior; neural plate of stage 15 Xenopus laevis embryos were isolated and normalized to stage 15 whole embryos. Three biological replicates were prepared for each tissue and the expression patterns were profiled using Affymetrix Xenopus Laevis GeneChip microarrays. Experiment Overall Design: Tissues from the eye primordia, lateral endoderm, and posterior Experiment Overall Design: neural plate of stage 15 Xenopus laevis embryos were isolated and normalized to stage 15 whole embryos. Three biological replicates were prepared for each tissue and the expression patterns were profiled using Affymetrix Xenopus Laevis GeneChip microarrays.

2009-09-15 | E-GEOD-9175 | biostudies-arrayexpress

Eye primordia vs. posterior neural plate vs. lateral endoderm normalized the whole embryos

Project description:Tissues from the eye primordia, lateral endoderm, and posterior neural plate of stage 15 Xenopus laevis embryos were isolated and normalized to stage 15 whole embryos. Three biological replicates were prepared for each tissue and the expression patterns were profiled using Affymetrix Xenopus Laevis GeneChip microarrays. Keywords: Three way comparison of Embryonic Tissue Isolation

2009-08-19 | GSE9175 | GEO

GNPS - Identification of a pharmaceutical biostasis inducer that slows metabolism in multiple vertebrates that do not hibernate (Thermal Proteome Profiling in Xenopus laevis)

Project description:DIA acquisition of Xenopus laevis embryo, using gas phase fractionation. DIA files were quantified on an extensive ion library. The library was generated using 3D fractionation of Xenopus embryos across several stages of development.

2023-03-04 | MSV000091410 | GNPS

Geminin loss causes neural tube defects through disrupted progenitor specification and neuronal differentiation.

Project description:Geminin is a nucleoprotein that can directly bind chromatin regulatory complexes to modulate gene expression during development. Geminin knockout mouse embryos are preimplantation lethal by the 32-cell stage, precluding in vivo study of Geminin's role in neural development. Therefore, here we used a conditional Geminin allele in combination with several Cre-driver lines to define an essential role for Geminin during mammalian neural tube (NT) formation and patterning. Geminin was required in the NT within a critical developmental time window (embryonic day 8.5-10.5), when NT patterning and closure occurs. Geminin excision at these stages resulted in strongly diminished expression of genes that mark and promote dorsal NT identities and decreased differentiation of ventral motor neurons, resulting in completely penetrant NT defects, while excision after embryonic day 10.5 did not result in NT defects. When Geminin was deleted specifically in the spinal NT, both NT defects and axial skeleton defects were observed, but neither defect occurred when Geminin was excised in paraxial mesenchyme, indicating a tissue autonomous requirement for Geminin in developing neuroectoderm. Despite a potential role for Geminin in cell cycle control, we found no evidence of proliferation defects or altered apoptosis. Comparisons of gene expression in the NT of Geminin mutant versus wild-type siblings at embryonic day 10.5 revealed decreased expression of key regulators of neurogenesis, including neurogenic bHLH transcription factors and dorsal interneuron progenitor markers. Together, these data demonstrate a requirement for Geminin for NT patterning and neuronal differentiation during mammalian neurulation in vivo.

| S-EPMC4134736 | biostudies-literature

Zebrafish embryos: Control MO vs. Lin28A MO vs. Lin28B MO injected

Project description:miRNA profiling of zebrafish embryos comparing control MO with Lin28A MO or Lin28B MO injected embryos at 5hpf

2013-11-19 | GSE52492 | GEO

SMN MO, Gemin2 MO knockdown vs Control MO injected

Project description:Transcriptiome profiling of SMN MO injected, Gemin2 MO injected zebrafish embryos vs Control MO injected Two condition experiment : MO injected vs control. Biological replicates for SMN MO injected : 6, Biological replicates for Gemin2 MO injected: 7; Control MO injected from 6 independent batches pooled to serve as common control sample in all arrays.

2013-12-05 | E-GEOD-47001 | biostudies-arrayexpress

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