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The salivary proteome in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients: a labelled and label-free proteomics approach -DIAdata

ABSTRACT: Decreased salivary flow rates and/or changes in protein composition reported after autologous hematopoietic stem cell transplantation (ASCT) reduces the protective function of saliva. This might be associated with the development of oral mucositis (OM), an inflammation of the oral mucosa as a result of chemotherapy before ASCT which affects patients, quality of life and risk factor for systemic infections. In this study, a TMT-labelled proteomics experiment, a label-free quantification (LFQ) proteomics experiment and a DIA-MS proteomics experiment were used to identify differences in the salivary proteome between patients with ulcerative OM (uOM; WHO score 2) and those without (nOM).

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human) Human Oral Bacteria Ensemble

TISSUE(S): Saliva

SUBMITTER: An Staes

LAB HEAD: Nicole M.A. Blijlevens

PROVIDER: PXD033525 | Pride | 2023-07-10

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20190924_100444_4513_HOMD_Human_LFQ__20190924_100444.kit	Other
	20191106_142045_PRC3908_all_HOMD_29102019_all103.sne	Other
	H082061_uPAC_5_PRC-3908_HuysmansLab_Shotgun_DIA_iRT_25x_Sample_Q1_20190404224052.raw	Raw
	H082063_uPAC_5_PRC-3908_HuysmansLab_Shotgun_DIA_iRT_25x_Sample_Q2_20190405030101.raw	Raw
	H082065_uPAC_5_PRC-3908_HuysmansLab_Shotgun_DIA_iRT_25x_Sample_Q3_20190405072117.raw	Raw

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Project description:Listeria monocytogenes is well known to have the ability to survive and grow under a variety of stress conditions. The ability to survive and grow under osmotic stress conditions in particular appears to be important for both growth in certain foods and food associated environments as well as for host infection. To characterize the contributions of transcriptional regulators important for stress response and virulence (i.e., Sigma B - M-OM-^CB and PrfA), we initially analyzed three L. monocytogenes parent strains and isogenic mutants ( delta sigB, delta prfA, and delta sigB delta prfA), representing different serotypes and lineages, for their ability to grow in BHI with 11% NaCl (1.9M) at 25M-BM-0C. No significant differences were observed in terms of growth between the parent strains and their respective mutants lacking prfA (i.e. delta prfA, and delta sigB delta prfA mutant strains). While for all strains, the delta sigB mutant showed a prolonged lag phase as compared to the parent strains, maximum growth rates were only reduced for the delta sigB mutant of lineage I and IV strains. Interestingly, for the serotype 1/2b strain, the delta sigB mutant reached a higher maximum cell density than the parent strain or the delta prfA mutant. Caco-2 intestinal epithelial cells invasion assays and hemolytic activity assays showed a significant role for M-OM-^CB in the former and for PrfA in the latter. To initially explore the mechanism that may contribute to the extended lag phase in the delta sigB mutant, microarray was performed to compare transcript levels between the lineage I, serotype 1/2b, parent strain and its isogenic delta sigB mutant in lag phase at 25M-BM-0C in the presence of 11% NaCl. Microarray data showed significant lower and higher transcript levels for 135 and 173 genes, respectively, in the parent strain as compared to the delta sigB strains. Overall, 51 of the 173 M-OM-^CB up-regulated genes had previously been found among the 249 M-OM-^CB-dependent genes identified in a microarray study conducted in stationary phase cells, indicating that up to 122 genes may be transcribed in a M-OM-^CB-dependent manner during lag phase under salt stress. Notable genes that showed higher transcript levels in the parent strain include inlD (encoding an internalin protein that may be involved in virulence), sigH (encoding an alternative M-OM-^C factor), glpK (encoding a glycerol kinase) and resD (encoding a two-component response regulator ResD); while, genes that showed lower transcript levels in the parent strain include dnaK (encoding a dihydroxyacetone kinase), groES (encoding a class I heat-shock protein GroES), grpE (encoding a co-chaperone GrpE) and fri (encoding a non-heme iron-binding ferritin). These data showed that although PrfA does not contribute to growth under osmotic stress at 25M-BM-0C, M-OM-^CB does contribute to survival of L. monocytogenes under high salt conditions. Moreover, the M-OM-^CB-dependent transcriptome of L. monocytogenes lag phase cells under salt stress was characterized and includes previously identified as well as novel M-OM-^CB-dependent genes, including a number of stress response and virulence-associated genes. Independent RNA isolations were performed for one wildtype (lineage I) and M-NM-^TsigB strains from cells grown to lag phase. Three biological replicates were used in competitive whole-genome microarray experiments. For each set of hybridizations, RNA from a L. monocytogenes wildtype strain was hybridized with RNA from its isogenic M-NM-^TsigB null mutant.

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The salivary proteome in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients: a labelled and label-free proteomics approach -DIAdata

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