Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LC-MS/MS-based Proteomics Approach for the Identification of Candidate Serum Biomarkers in Patients with Narcolepsy Type 1

ABSTRACT: The study is based on the identification of serum protein biomarkers for NT 1. A total of 27 serum samples were collected (16 NT 1 and 11 controls), the altered expression levels of low-abundant proteins (DEPs) associated with narcolepsy type 1 was investigated by comparing the proteomes of the two sample cohorts. DEPs that are revealed to be most related to NT 1 pathogenesis and have high levels of fold changes were further targeted and validated by LC-PRM-MS. Then, the effects of the DEPs were explored by system biology analysis.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Serum

DISEASE(S): Narcolepsy

SUBMITTER: Akeem Sanni

LAB HEAD: Yehia Mechref

PROVIDER: PXD038248 | Pride | 2023-05-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	10FF_NT1_PRM.mzid.gz	Mzid
	10FF_PRM_1Ug_7_27_22.mgf	Mgf
	10FF_PRM_1Ug_7_27_22.raw	Raw
	11DSG_NT1_PRM.mzid.gz	Mzid
	11DSG_NTI_PRM_1Ug_7_27_22.mgf	Mgf

Items per page:

1 - 5 of 162

Publications

LC-MS/MS-Based Proteomics Approach for the Identification of Candidate Serum Biomarkers in Patients with Narcolepsy Type 1.

Sanni Akeem A Goli Mona M Zhao Jingfu J Wang Junyao J Barsa Chloe C El Hayek Samer S Talih Farid F Lanuzza Bartolo B Kobeissy Firas F Plazzi Giuseppe G Moresco Monica M Mondello Stefania S Ferri Raffaele R Mechref Yehia Y

Biomolecules 20230223 3

Narcolepsy type 1 (NT1) is the most common type of narcolepsy known to be caused by the loss of specific neurons responsible for producing peptide neurotransmitters (orexins/hypocretins), resulting in a sleep-wake cycle disorder. It is characterized by its association with cataplexy and abnormalities in rapid eye movement. To date, no cure has been established for this life-threatening condition. Misdiagnosis of NT1 is also quite common, although it is not exceedingly rare. Therefore, successful ...[more]

PMID: 36979356

Similar Datasets

Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover

Project description:Protein N-terminal (Nt) acetylation is one of the most abundant modifications in eukaryotes, covering ~50-80 % of the proteome, depending on species. Cells with defective Nt-acetylation display a wide array of phenotypes such as impaired growth, mating defects and increased stress sensitivity. However, the pleiotropic nature of these effects has hampered our understanding of the functional impact of protein Nt-acetylation. The main enzyme responsible for Nt-acetylation throughout the eukaryotic kingdom is the N-terminal acetyltransferase NatA. Here we employed a multi-dimensional proteomics approach to analyze Saccharomyces cerevisiae lacking NatA activity, which caused global proteome remodeling. Pulsed-SILAC experiments revealed that NatA-deficient strains consistently increased degradation of ribosomal proteins compared to wild type. Explaining this phenomenon, thermal proteome profiling uncovered decreased thermostability of ribosomes in NatA-knockouts. Our data are in agreement with a role for Nt-acetylation in promoting stability for parts of the proteome by enhancing the avidity of protein-protein interactions and folding.

2023-10-24 | PXD037510 | Pride

iTRAQ analyses of Fe-sufficient and Fe-deficient non-transformant and HRZ-knockdown rice roots

Project description:We conducted iTRAQ analyses using soluble proteins extracted from roots of non-transformant rice (NT) and previously generated HRZ-knockdown (HRZi) lines (Kobayashi et al., 2013 Nat Commun 4: 2792) cultivated under Fe-sufficient and Fe-deficient conditions. We identified and quantified 3,033 and 3,525 proteins in replicate 1 and 2, respectively, which totaled 4,884 proteins including 1,698 overlapping proteins between the two replicate experiments.

2022-04-08 | PXD026597 | Pride

DEPS-1 promotes P granule assembly and RNA interference in C. elegans germ cells

Project description:P granules are germ-cell-specific cytoplasmic structures containing RNA and protein and required for proper germ cell development in C. elegans. A new P-granule-associated protein, DEPS-1, whose loss disrupts P granule structure and function was analysed in this study. Genome wide analysis of gene expression in deps-1 mutant germ lines identified additional targets of DEPS-1 regulation, many of which are also regulated by the RNAi factor RDE-3. Our studies suggest that DEPS-1 is a key component of the P granule assembly pathway and that its roles include promoting accumulation of some mRNAs, such as glh-1 and rde-4, and reducing accumulation of other mRNAs, perhaps by collaborating with RDE-3 to generate endogenous short interfering RNAs (endo-siRNAs). We isolated dissected gonads from deps-1 mutant adults and compared each to wild type dissected gonads. RNA was linearly amplified prior to labeling for all genotypes. The comparisons were done in quadruplicate on independently grown and isolated animals.

2010-05-26 | E-GEOD-9993 | biostudies-arrayexpress

Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana

Project description:We grafted Transcriptional Gene Silencing (TGS)-inducing wild type Arabidopsis and a mutant that is compromised in 24 nucleotide (nt) small RNA (sRNA) production onto a wild type reporter line. We observed that 21-24 nt sRNAs were transmitted across a graft union yet only the 24 nt sRNAs directed RNA-dependent DNA methylation (RdDM) and TGS of a transgene promoter in meristematic cells. Analysis of sRNAs associated with mobile TGS by deep sequencing, biological replicates. 10 unique samples, 5 biological replicates.

2011-10-23 | E-GEOD-31651 | biostudies-arrayexpress

Metabolic regulation of N-terminal acetylation in yeast

Project description:N-terminal (Nt) acetylation, catalyzed by N-terminal acetyltransferases (NATs), has emerged as an important co-translational modification in eukaryotes, and involves the transfer of the acetyl moiety from acetyl-CoA (Ac-CoA) to the α-amino group of a nascent polypeptide. Here, we report the first global study of Nt-acetylation in response to changes in nutrient availability in S. cerevisiae. Despite major fluctuations in Ac-CoA and histone acetylation levels, our study reveals that the steady-state levels of protein Nt-acetylation remains largely unaffected by changes in cellular metabolism. Accordingly, Ac-CoA does not appear to act as a master switch for protein Nt-acetylation. Interestingly however, we identified two distinct sets of N-termini that are differentially Nt-acetylated following nutrient starvation. The first set of proteins, enriched for annotated N-termini, generally displayed an increased Nt-acetylation in stationary phase compared to exponential growth phase, despite a significant reduction in Ac-CoA levels. In contrast, the second set of proteins, enriched for alternative non-annotated N-termini (i.e. N-terminal proteoforms), generally became less acetylated in stationary phase. In particular, the degree of Nt-acetylation of Pcl8, a negative regulator of glycogen biosynthesis and two components of the pre-ribosome complex (Rsa3 and Rpl7a) increased during starvation. Moreover, the levels of these proteins were regulated by both starvation and the presence of NatA activity. Overall, our data provide the first proteome-wide survey on metabolic regulation of Nt-acetylation, and propose Nt-acetylation-mediated steering of metabolism and ribosome biogenesis.

2018-09-07 | PXD004326 | Pride

DEPS-1

Project description:DEPS-1 smallRNA

| PRJEB24820 | ENA

DEPS-1 promotes P granule assembly and RNA interference in C. elegans germ cells

Project description:P granules are germ-cell-specific cytoplasmic structures containing RNA and protein and required for proper germ cell development in C. elegans. A new P-granule-associated protein, DEPS-1, whose loss disrupts P granule structure and function was analysed in this study. Genome wide analysis of gene expression in deps-1 mutant germ lines identified additional targets of DEPS-1 regulation, many of which are also regulated by the RNAi factor RDE-3. Our studies suggest that DEPS-1 is a key component of the P granule assembly pathway and that its roles include promoting accumulation of some mRNAs, such as glh-1 and rde-4, and reducing accumulation of other mRNAs, perhaps by collaborating with RDE-3 to generate endogenous short interfering RNAs (endo-siRNAs). Keywords: Mutant analysis of deps-1 dissected C. elegans gonads

2008-02-01 | GSE9993 | GEO

DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV

Project description:DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase Pol IV transcribes target sequences to initiate 24-nt siRNA production and action. The Arabidopsis DTF1/SHH1 has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and mechanism of DTF1 function in RdDM is unclear. We show here that DTF1 is necessary for the accumulation of the majority of Pol IV-dependent 24-nt siRNAs. It is also required for a large proportion of Pol IV-dependent de novo DNA methylation. Interestingly, there is a group of RdDM target loci where 24-nt siRNA accumulation but not DNA methylation is dependent on DTF1. Taken together, our results show that DTF1 is a core component of the RdDM pathway. Our results also suggest the involvement of DTF1 in an important negative feedback mechanism for DNA methylation at some RdDM target loci. Examination of whole-genome DNA methylation and small RNA in 12-day-old Col-0, dtf1-2, nrpd1-3 and nrpe1-11 seedlings

2013-06-03 | E-GEOD-44209 | biostudies-arrayexpress

Lymph miRNA in FcgRIIA transgenic mice, in K/BxN rheumatoid arthritis

Project description:Thoracic lymph was collected from FcgRIIA transgenic mice, after 7 day of K/BxN arthritis. Cells were removed by centrifugation, and extra-cellular microRNAs were assessed by short RNA Illumina sequencing (Arraystar Inc, 16-30 nt). 3 control (injected with PBS) and 3 K/BxN (injected I.P. with 150 µL of K/BxN serum on day 0 and day 2) mice were respectively pooled in one biological sample for sequencing.

2020-04-02 | E-MTAB-8171 | biostudies-arrayexpress

Tuber-omics in potato with the T and D types of cytoplasm showed differentially expressed genes and proteins in response to cold storage

Project description:For the first time, we report differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in potato (Solanum tuberosum L.) tubers characterized by light and dark chip color after cold storage. Two potato diploid progenies derived from reciprocal crosses of parental clones possessing the T- and D-type cytoplasm were used. We recognized 48 and 15 DEGs as compared to RNA-seq data of contrasting segregants. We identified DEPs in potato tuber amyloplast and mitochondrial fractions. Seven and five DEPs were identified in the amyloplast fractions of the T – and D – type cytoplasm, respectively. Higher number of DEPs were selected from the mitochondrial fraction. The corresponding values were 97 and 105, including 39 common DEPs in the T – and D – type cytoplasm. These findings suggest that mitochondria may play a more important role than amyloplasts in response of potato tubers to cold treatment and that this influence can be different for the T – and D – type cytoplasm. However, we showed that the mt/nucDNA and pt/nucDNA ratios tend to increase for tubers characterized by dark chip color when compared with light chip color samples. Therefore, a protective effect of reducing sugars on both amyloplasts and mitochondria during low temperature treatment should be considered.

2021-09-17 | GSE184141 | 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