bims-prodis 2018-10-28 papers

Issue of 2018‒10‒28
three papers selected by
Nancy Gough
Bioserendipity

J Proteomics. 2018 Oct 18. pii: S1874-3919(18)30375-0. [Epub ahead of print]

Strategies for managing multi-patient 3D mass spectrometry imaging data.

D R N Vos, I Jansen, M Lucas, M R L Paine, O J de Boer, S L Meijer, C D Savci-Heijink, H Marquering, D M de Bruin, R M A Heeren, S R Ellis, B Balluff.

Mass spectrometry imaging (MSI) has emerged as a powerful tool in biomedical research to reveal the localization of a broad scale of compounds ranging from metabolites to proteins in diseased tissues, such as malignant tumors. MSI is most commonly used for the two-dimensional imaging of tissues from multiple patients or for the three-dimensional (3D) imaging of tissue from a single patient. These applications are potentially introducing a sampling bias on a sample or patient level, respectively. The aim of this study is therefore to investigate the consequences of sampling bias on sample representativeness and on the precision of biomarker discovery for histological grading of human bladder cancers by MSI. We therefore submitted formalin-fixed paraffin-embedded tissues from 14 bladder cancer patients with varying histological grades to 3D analysis by matrix-assisted laser desorption/ionization (MALDI) MSI. We found that, after removing 20% of the data based on novel outlier detection routines for 3D-MSI data based on the evaluation of digestion efficacy and z-directed regression, on average 33% of a sample has to be measured in order to obtain sufficient coverage of the existing biological variance within a tissue sample. SIGNIFICANCE: In this study, 3D MALDI-MSI is applied for the first time on a cohort of bladder cancer patients using formalin-fixed paraffin-embedded (FFPE) tissue of bladder cancer resections. This work portrays the reproducibility that can be achieved when employing an optimized sample preparation and subsequent data evaluation approach. Our data shows the influence of sampling bias on the variability of the results, especially for a small patient cohort. Furthermore, the presented data analysis workflow can be used by others as a 3D FFPE data-analysis pipeline working on multi-patient 3D-MSI studies.

Keywords: 3-dimensional; Bladder cancer; Formalin-fixed paraffin-embedded tissue; Mass spectrometry imaging; Sampling bias

DOI: https://doi.org/10.1016/j.jprot.2018.10.008

Neurobiol Aging. 2018 Sep 25. pii: S0197-4580(18)30343-9. [Epub ahead of print]73 123-134

Unveiling the olfactory proteostatic disarrangement in Parkinson's disease by proteome-wide profiling.

Mercedes Lachén-Montes, Andrea González-Morales, Ibon Iloro, Felix Elortza, Isidre Ferrer, Djordje Gveric, Joaquín Fernández-Irigoyen, Enrique Santamaría.

Olfactory dysfunction is one of the earliest features in Lewy-type alpha-synucleinopathies (LTSs) such as Parkinson's disease (PD). However, the underlying molecular mechanisms associated to smell impairment are poorly understood. Applying mass spectrometry-based quantitative proteomics in postmortem olfactory bulbs across limbic, early-neocortical, and neocortical LTS stages of parkinsonian patients, a proteostasis impairment, was observed, identifying 268 differentially expressed proteins between controls and PD phenotypes. In addition, network-driven proteomics revealed a modulation in ERK1/2, MKK3/6, and PDK1/PKC signaling axes. Moreover, a cross-disease study of selected olfactory molecules in sporadic Alzheimer's disease (AD) cases revealed different protein derangements in the modulation of secretagogin (SCGN), calcyclin-binding protein (CACYBP), and glucosamine 6 phosphate isomerase 2 (GNPDA2) between PD and AD. An inverse correlation between GNPDA2 and α-synuclein protein levels was also reflected in PD cerebrospinal fluid. Interestingly, PD patients exhibited significantly lower serum GNPDA2 levels than controls (n = 82/group). Our study provides important avenues for understanding the olfactory bulb proteostasis imbalance in PD, deciphering mechanistic clues to the equivalent smell deficits observed in AD and PD pathologies.

Keywords: Olfactory bulb; Parkinson's disease; Proteomics; Systems biology

DOI: https://doi.org/10.1016/j.neurobiolaging.2018.09.018

Biochimie. 2018 Oct 17. pii: S0300-9084(18)30287-6. [Epub ahead of print]

Influence of Passage Number on the Impact of the Secretome of Adipose Tissue Stem Cells on Neural Survival, Neurodifferentiation and Axonal Growth.

Sofia C Serra, João C Costa, Rita C Assunção-Silva, Fábio G Teixeira, Nuno A Silva, Sandro I Anjo, Bruno Manadas, Jeffrey Gimble, Leo A Behie, António J Salgado.

Mesenchymal stem cells (MSCs), and within them adipose tissue derived stem cells (ASCs), have been shown to have therapeutic effects on central nervous system (CNS) cell populations. Such effects have been mostly attributed to soluble factors, as well as vesicles, present in their secretome. Yet, little is known about the impact that MSC passaging might have in the secretion therapeutic profile. Our aim was to show how human ASCs (hASCs) passage number influences the effect of their secretome in neuronal survival, differentiation and axonal growth. For this purpose, post-natal rat hippocampal primary cultures, human neural progenitor cell (hNPCs) cultures and dorsal root ganglia (DRGs) explants were incubated with secretome, collected as conditioned media (CMs), obtained from hASCs in P3, P6, P9 and P12. Results showed no differences when comparing percentages of MAP-2 positive cells (a mature neuronal marker) in neuronal cultures or of hNPCs that differentiated, after incubation with hASCs secretome from different passages. The same was observed regarding DRG neurite outgrowth. In order to characterize the secretomes obtained from different passages, a proteomic analysis was performed, revealing that its composition did not vary significantly with passage number P3 to P12. Results allowed us to identify several key proteins, such as pigment epithelium derived factor (PEDF), DJ-1, interleucin-6 (IL-6) and galectin, all of which have already proven to play neuroprotective and neurodifferentiating roles. Proteins that promote neurite outgrowth were also found present, such as semaphorin 7A and glypican-1. We conclude that cellular passaging does not influence significantly hASC's secretome properties especially their ability to support post-natal neuronal survival, induce neurodifferentiation and promote axonal growth.

Keywords: Adipose Tissue Stem Cells; Axonal Growth; Central Nervous System; Differentiation; Keyords: Secretome; Proteomics

DOI: https://doi.org/10.1016/j.biochi.2018.09.012