Antigen retrieval prior to on-tissue digestion of formalin-fixed paraffin-embedded tumour tissue sections yields oxidation of proline residues

Djidja, Marie-Claude; Claude, Emmanuelle; Scriven, Peter; Allen, David W.; Carolan, Vikki A.; Clench, Malcolm R.

doi:10.1016/j.bbapap.2016.11.019

Cited by 16 publications

(15 citation statements)

References 22 publications

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“…The tissue samples were fixed in 10% neutral buffered formalin and processed for histology and immunohistochemistry via paraffin embedding after which they were sectioned at 4 μm using a Thermo Scientific HM 325 rotatory microtome (CE Bright Company Ltd. Huntington England), cleared in xylene and hydrated in decreasing alcohols, stained with Hematoxylin and Eosin (H&E) and mounted with DPX (Djidja et al, 2017). The histological specimen were captured and examined using the Leica SlidePath Gateway LAN software.…”

Section: Methodsmentioning

confidence: 99%

Combination antiretroviral therapy (cART)-induced hippocampal disorders: Highlights on therapeutic potential of Naringenin and Quercetin

et al. 2019

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HighlightsNaringenin and Quercetin decrease ROS and potentiate enzymatic antioxidant production in the hippocampus.cART induced marked cytoplasmic shrinkage and several pyknotic nuclei in the dentate gyrus and cornus ammonis region.Naringenin and Quercetin attenuates cART-induced upregulation of monoamine oxidase-B expression in neurons.Naringenin and Quercetin also ameliorates cART-induced spatial memory impairments.Naringenin and Quercetin acted as effective antioxidants in vivo against cART-induced neurotoxicity.

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Section: Methodsmentioning

confidence: 99%

Combination antiretroviral therapy (cART)-induced hippocampal disorders: Highlights on therapeutic potential of Naringenin and Quercetin

et al. 2019

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“…After removal of the tissue from the body, tissue samples should be immediately snap-frozen in 2-methyl-butane (isopentane) and stored at -80 °C until use. For MSI of proteins, fresh frozen tissue is preferred over alcohol-preserved, or formaldehyde-fixated and paraffin-embedded (FFPE) tissue sections, because of the covalent crosslinking of proteins in FFPE sections or precipitated proteins in alcohol-preserved sections, although recently the antigen retrieval strategy has been suggested to overcome the protein crosslinks in FFPE sections 30,31 . In all cases, tissue sections with a thickness of approximately 10 μm are prepared with a microcryotome.…”

Section: Tissue Sample Preparationmentioning

confidence: 99%

Imaging of protein distribution in tissues using mass spectrometry: An interdisciplinary challenge

Han

Permentier

Bischoff

et al. 2019

TrAC Trends in Analytical Chemistry

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The recent development of mass spectrometry imaging (MSI) technology allowed to obtain highly detailed images of the spatial distribution of proteins in tissue at high spatial resolution reaching cell dimensions, high target specificity and a large dynamic concentration range. This review focusses on the development of two main MSI principles, targeted and untargeted detection of protein distribution in tissue samples, with special emphasis on the improvements in analyzed mass range and spatial resolution over the last 10 years. Untargeted MSI of in situ digested proteins with matrix-assisted laser desorption ionization is the most widely used approach, but targeted protein MSI technologies using laser ablation inductively coupled plasma (LA-ICP) and photocleavable mass tag chemical labeling strategies are gaining momentum. Moreover, this review also provides an overview of the effect of sample preparation on image quality and the bioinformatic challenge to identify proteins and quantify their distribution in complex MSI data.

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“…Based upon the nature of fixative, formalin fixation and antigen retrieval lead to chemical modifications and molecular differences between FFPE and PFPE tissues 18,19,33 .…”

Section: Accepted Manuscriptmentioning

confidence: 99%

PAXgene fixation enables comprehensive metabolomic and proteomic analyses of tissue specimens by MALDI MSI

Urban

Buck

Siveke

et al. 2018

Biochimica et Biophysica Acta (BBA) - General Subjects

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An alcohol-based non-crosslinking tissue fixative, PAXgene Tissue System, has been proposed as alternative fixation method to formalin, providing superior and morphological preservation. To date, metabolites have not been assessed in PAXgene-fixed tissues. The study focuses on a comparison between PAXgene and standard formalin fixation for metabolomic analysis by MALDI mass spectrometry imaging. Therefore, fifty-six samples from seven mice organs were fixed with PAXgene (PFPE) or formalin (FFPE), embedded in paraffin, and processed to a tissue microarray. PAXgene was able to spatially preserve metabolites in organs achieving an overlap of common metabolites ranging from 34 to 78% with FFPE. Highly similar signal intensities and visualization of molecules demonstrated negligible differences for metabolite imaging on PFPE compared to FFPE tissues. In addition, we performed proteomic analysis of intact proteins and peptides derived from enzymatic digestion. An overlap of 33 to 58% was found between FFPE and PFPE tissue samples in peptide analysis with a higher number of PFPE-specific peaks. Analysis of intact proteins achieved an overlap in the range of 0 to 28% owing to the poor detectability of cross-linked proteins in formalin-fixed tissues. Furthermore, metabolite and peptide profiles obtained from PFPE tissues were able to correctly classify organs independent of the fixation method, whereas a distinction of organs by protein profiles was only achieved by PAXgene fixation. Finally, we applied MALDI MSI to human biopsies by sequentially analyzing metabolites and peptides within the same tissue section. Concerning prospective studies, PAXgene can be used as an alternative fixative for multi-omic tissue analysis.

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Antigen retrieval prior to on-tissue digestion of formalin-fixed paraffin-embedded tumour tissue sections yields oxidation of proline residues

Cited by 16 publications

References 22 publications

Combination antiretroviral therapy (cART)-induced hippocampal disorders: Highlights on therapeutic potential of Naringenin and Quercetin

Combination antiretroviral therapy (cART)-induced hippocampal disorders: Highlights on therapeutic potential of Naringenin and Quercetin

Imaging of protein distribution in tissues using mass spectrometry: An interdisciplinary challenge

PAXgene fixation enables comprehensive metabolomic and proteomic analyses of tissue specimens by MALDI MSI

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