Dataset Information

Proteomics analysis of stool samples from preterm neonates with mass spectrometry for predicting necrotizing enterocolitis

ABSTRACT: This study aimed to investigate the potential of fecal proteomics signatures for NEC prediction. Stools were collected from NEC infants up to 10 days before their diagnosis and matched with those from non-NEC controls for three tested periods. Stool samples were analyzed with liquid chromatography-tandem mass spectrometry using SWATH acquisition and a cross-compatible proteomic software platform to perform label-free quantification. ROC curves and principal component analysis were used to explore discriminating information provided by potential markers and sets of markers were evaluated with classical clustering and classification methods to evaluate their capacity to sort the samples giving to their actual outcomes. We identified a specific series of markers that predicted all NEC from non-NEC infants at least a week in advance. Our study shows that multiplexed proteomic signature detection constitutes a favorable approach for the early detection of NEC.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Feces

DISEASE(S): Perinatal Necrotizing Enterocolitis

SUBMITTER: David Gagne

LAB HEAD: Jean-François Beaulieu

PROVIDER: PXD036178 | Pride | 2023-03-11

REPOSITORIES: pride

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Dataset's files

Source:

			Action	DRS
	1089_UniprotEntry.fasta	Fasta
	1_FragPipe_SEARCH_SamplesPool_DDA.zip	Other
	2_FragPipe_SEARCH_42Samples_SWATH.zip	Other
	3_FragPipe_SEARCH_DDASWATH.zip	Other
	DIANN_1089_prots_QUANT.zip	Other

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Publications

Proteomics Profiling of Stool Samples from Preterm Neonates with SWATH/DIA Mass Spectrometry for Predicting Necrotizing Enterocolitis.

Gagné David D Shajari Elmira E Thibault Marie-Pier MP Noël Jean-François JF Boisvert François-Michel FM Babakissa Corentin C Levy Emile E Gagnon Hugo H Brunet Marie A MA Grynspan David D Ferretti Emanuela E Bertelle Valérie V Beaulieu Jean-François JF

International journal of molecular sciences 20221001 19

Necrotizing enterocolitis (NEC) is a life-threatening condition for premature infants in neonatal intensive care units. Finding indicators that can predict NEC development before symptoms appear would provide more time to apply targeted interventions. In this study, stools from 132 very-low-birth-weight (VLBW) infants were collected daily in the context of a multi-center prospective study aimed at investigating the potential of fecal biomarkers for NEC prediction using proteomics technology. Eig ...[more]

PMID: 36232903

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Project description:In somatic embryogenesis, embryos are formed from a single or small group of somatic cells in response to stress and hormonal stimuli. In this study, a high-throughput phosphoproteomic analysis was used to identify and quantify phosphoproteins related to the acquisition of embryogenic competence in sugarcane. Embryogenic (EC) and nonembryogenic (NEC) calli were compared at the multiplication phase, resulting in the identification of 1279 phosphoproteins. After the differential accumulation analysis, 163 phosphoproteins were identified as unique to EC, and nine were unique to NEC, while 51 were upaccumulated, and 40 were downaccumulated in EC compared to NEC. These phosphopeptides were mainly single phosphorylated peptides, with serine residues representing the major site of phosphorylation. The motif-x analysis revealed the enrichment of [xxxpSPxxx], [RxxpSxxx] and [xxxpSDxxx] motifs, which are predicted phosphorylation sites for several kinases related to stress responses. Gene ontology enrichment revealed an overrepresentation of biological processes involved in embryonic development, showing that EC-related phosphoproteins (unique to EC and upaccumulated) were associated with stress responses, regulation of gene expression and epigenetic modifications. The NEC-related phosphoproteins (unique to NEC and downaccumulated) were associated with the translation process. In this sense, EC-related phosphoproteins described as potential regulators of abiotic stress tolerance in response to ABA-induced signals such as OSK3 (a catalytic subunit of SnRK1), ABF1, LEAs, REM4.1 and RD29Bs were identified. On the other hand, the NEC-related phosphoproteins EDR1 and PP2Ac-2 were negative regulators of ABA, suggesting a role of ABA in the acquisition of embryogenic competence linked to stress tolerance. Moreover, EC-related phosphoproteins associated with epigenetic modifications, such as HDA6, HDA19, and TPL, as well as those involved in embryo development, including ASIL1, M3KE1, MCM2, and GRV2, were identified as putative potential regulators of embryogenic competence. Our results provide novel data that may help elucidate the phosphorylation mechanisms controlling the activity, affinity and localization of specific proteins during somatic embryogenesis and suggest a role for these proteins in the hormonal signalling cascade leading to stress adaptation by reprogramming genetic expression.