Dataset Information

Identification of proteomic markers in head and neck cancer using MALDI-MS Imaging, LC-MS/MS and IHC

ABSTRACT: Purpose The heterogeneity of squamous cell carcinoma tissue complicates diagnosis and an individualized therapy to a great extent. Therefore it is of utmost importance to spatially characterize this tissue heterogeneity and to identify appropriate biomarkers. Matrix assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) can analyze spatially resolved tissue biopsies on a molecular level. Experimental design MALDI MSI of snap frozen tissues as well as of formalin-fixed and paraffin-embedded (FFPE) tissue samples from patients with head and neck cancer (HNC) were used to analyze m/z values localized in tumor and non-tumor regions. Peptide identification was performed by using liquid chromatography (LC)-MS/MS and immunohistochemistry (IHC). Results In both FFPE and frozen tissue specimen seven characteristic masses of the tumor epithelial region were found identified. Using LC-MS/MS, the peaks were identified as Vimentin, Keratin type II, Nucleolin, Heat shock protein 90, Prelamin-A/C, Junction plakoglobin and PGAM1. Finally, Vimentin, Nucleolin and PGAM1 were verified with IHC. Conclusions and Clinical Relevance The combination of MALDI MSI, LC-MS/MS and subsequent IHC is an appropriate tool to characterize the molecular heterogeneity of tissue as well as to identify new representative biomarkers for a more individualized therapy.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Head, Neck

DISEASE(S): Head And Neck Cancer

SUBMITTER: Thomas Krüger

LAB HEAD: Olaf Kniemeyer

PROVIDER: PXD009144 | Pride | 2018-11-14

REPOSITORIES: Pride

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Identification of Proteomic Markers in Head and Neck Cancer Using MALDI-MS Imaging, LC-MS/MS, and Immunohistochemistry.

Hoffmann Franziska F Umbreit Claudia C Krüger Thomas T Pelzel Daniela D Ernst Günther G Kniemeyer Olaf O Guntinas-Lichius Orlando O Berndt Alexander A von Eggeling Ferdinand F

Proteomics. Clinical applications 20181126 1

<h4>Purpose</h4>The heterogeneity of squamous cell carcinoma tissue greatly complicates diagnosis and individualized therapy. Therefore, characterizing the heterogeneity of tissue spatially and identifying appropriate biomarkers is crucial. MALDI-MS imaging (MSI) is capable of analyzing spatially resolved tissue biopsies on a molecular level.<h4>Experimental design</h4>MALDI-MSI is used on snap frozen and formalin-fixed and paraffin-embedded (FFPE) tissue samples from patients with head and neck ...[more]

PMID: 30411850

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Project description:Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has recently gained prominence for its ability to provide molecular and spatial information in tissue sections. This technology has the potential to uncover novel insights into proteins and other molecules in biological and immunological pathways activated along diseases with a complex host-pathogen interaction, such as animal tuberculosis. Thus, the present study conducted a data analysis of protein signature in granulomas of cattle and pigs naturally infected with Mycobacterium tuberculosis complex (MTC), identifying biological and immunological signalling pathways activated throughout the disease. Lymph nodes from four pigs and cattle, positive for MTC by bacteriological culture and/or real-time PCR, were processed for histopathological examination and MALDI-MSI. Protein identities were assigned using the MaTisse database, and protein-protein interaction networks were visualized using the STRING database. Gene ontology (GO) analysis was carried out to determine biological and immunological signalling pathways in which these proteins could participate together with KEGG analysis. Distinct proteomic profiles between cattle and pig granulomas were displayed. Noteworthy, the GO analysis revealed also common pathways among both species, such as â€œComplement activation, alternative pathwayâ€� and â€œTricarboxylic acid cycleâ€�, which highlights pathways that are conserved among different species infected by MTC. In addition, species-specific terms were identified in the current study, such as â€œNatural killer cell degranulationâ€� in cattle or those related to platelet and neutrophils recruitment and activation in pigs. Overall, this study provides insights into the immunopathogenesis of tuberculosis in cattle and pigs, opening new areas of research and highlighting the importance, among others, of the complement activation pathway and the regulation of natural killer cell and neutrophil-mediated immunity in this disease.

			Action	DRS
	02-1-a.raw	Raw
	02-1-b.raw	Raw
	02-1.fasta	Fasta
	02-1.mgf	Mgf
	02-1.msf	Msf