Papers by Pierre Chaurand
Journal of Cheminformatics, Jul 22, 2020
Mass spectrometry imaging (MSI) has become a mature, widespread analytical technique to perform n... more Mass spectrometry imaging (MSI) has become a mature, widespread analytical technique to perform non-targeted spatial metabolomics. However, the compounds used to promote desorption and ionization of the analyte during acquisition cause spectral interferences in the low mass range that hinder downstream data processing in metabolomics applications. Thus, it is advisable to annotate and remove matrix-related peaks to reduce the number of redundant and non-biologically-relevant variables in the dataset. We have developed rMSIcleanup, an open-source R package to annotate and remove signals from the matrix, according to the matrix chemical composition and the spatial distribution of its ions. To validate the annotation method, rMSIcleanup was challenged with several images acquired using silver-assisted laser desorption ionization MSI (AgLDI MSI). The algorithm was able to correctly classify m/z signals related to silver clusters. Visual exploration of the data using Principal Component Analysis (PCA) demonstrated that annotation and removal of matrix-related signals improved spectral data post-processing. The results highlight the need for including matrix-related peak annotation tools such as rMSIcleanup in MSI workflows.
Journal of Proteome Research, Nov 11, 2009
Human tissues are an important source of biological material for the discovery of novel biomarker... more Human tissues are an important source of biological material for the discovery of novel biomarkers. Fresh-frozen tissue could represent an ideal supply of archival material for molecular investigations. However, immediate flash freezing is usually not possible, especially for rare or valuable tissue samples such as biopsies. Here, we investigated the compatibility of RCL2/CS100, a non-crosslinking, non-toxic, and non-volatile organic fixative, with shotgun proteomic analyses. Several protein extraction protocols compatible with mass spectrometry were investigated from RCL2/CS100-fixed and fresh-frozen colonic mucosa, breast, and prostate tissues. The peptides and proteins identified from RCL2/CS100 tissue were then comprehensively compared with those identified from matched fresh-frozen tissues using a bottom-up strategy based on nano-reversed phase liquid chromatography coupled with tandem mass spectrometry (nanoRPLC-MS/MS). Results showed that similar peptides could be identified in both archival conditions and the proteome coverage was not obviously compromised by the RCL2/CS100 fixation process. NanoRPLC-MS/MS of laser capture microdissected RCL2/CS100-fixed tissues gave the same amount of biological information as that recovered from whole RCL2/CS100-fixed or frozen tissues. We next performed MALDI tissue profiling and imaging mass spectrometry and observed a high level of agreement in protein expression as well as excellent agreement between the images obtained from RCL2/CS100-fixed and fresh-frozen tissue samples. These results suggest that RCL2/CS100-fixed tissues are suitable for shotgun proteomic analyses and tissue imaging. More importantly, this alternate fixative opens the door to the analysis of small, valuable, and rare target lesions that are usually inaccessible to complementary biomarker-driven genomic and proteomic research.
Analytical and Bioanalytical Chemistry, Dec 5, 2018
Hepatic lipid accumulation, mainly in the form of triglycerides (TGs), is the hallmark of nonalco... more Hepatic lipid accumulation, mainly in the form of triglycerides (TGs), is the hallmark of nonalcoholic fatty liver disease (NAFLD). To date, the spatial distribution of individual lipids in NAFLD affected livers is not well characterized. This study aims to map the triglyceride distribution in normal human liver samples and livers with NAFLD and cirrhosis with imaging mass spectrometry (MALDI IMS). Specifically, whether individual triglyceride species differing by fatty acid chain length and degree of saturation correlate with the histopathological features of NAFLD as identified with classical H&E. Using a recently reported sodium doped gold-assisted laser desorption/ionization IMS sample preparation, twenty human liver samples (five normal livers, five samples with simple steatosis, five samples with steatohepatitis, and five samples with cirrhosis) were analyzed at 10 μm lateral resolution. A total of 24 individual lipid species, primarily neutral lipids, were identified (22 TGs and 2 phospholipids). In samples with a low level of steatosis, TGs accumulated around the pericentral zone. In all samples, TGs with different degrees of side-chain saturation and side-chain length demonstrated differential distribution. Furthermore, hepatocytes containing macro lipid droplets were highly enriched in fully saturated triglycerides. This enrichment was also observed in areas of hepatocyte ballooning in samples with steatohepatitis and cirrhosis. In conclusion, macro lipid droplets in NAFLD are enriched in fully saturated triglycerides, indicating a possible increase in de novo lipogenesis that leads to steatohepatitis and cirrhosis.
Mass Spectrometry Imaging dataset of mouse brain sample and fingermark to be used as sample datas... more Mass Spectrometry Imaging dataset of mouse brain sample and fingermark to be used as sample dataset in to demonstrate the functionality of rMSIcleanup (https://github.com/gbaquer/rMSIcleanup). Acquired with silver-assisted LDI using MALDI TOF/TOF ultrafleXtreme. The datasets are referred to as Dataset 11 (141106_BookMouseBrain_Silver) and Dataset 12 (141129_Fingermark_Silver_Porous) in the accompanying publication (https://doi.org/10.1101/2019.12.20.884957 ). Due to its large file size, Dataset 12 (150209_Fingermark_75 um) can only be accessed upon request to the corresponding author. An alternative dataset (141129_Fingermark_Silver_Porous) with the same sample type and acquisition parameters but with considerably smaller file size has been made publicly available instead
Journal of Mass Spectrometry, Jun 24, 2014
Imaging mass spectrometry (IMS) is useful for visualizing the localization of phospholipids on bi... more Imaging mass spectrometry (IMS) is useful for visualizing the localization of phospholipids on biological tissue surfaces creating great opportunities for IMS in lipidomic investigations. With advancements in IMS of lipids, there is a demand for large-scale tissue studies necessitating stable, efficient and well-defined sample handling procedures. Our work within this article shows the effects of different storage conditions on the phospholipid composition of sectioned tissues from mouse organs. We have taken serial sections from mouse brain, kidney and liver thaw mounted unto ITO-coated glass slides and stored them under various conditions later analyzing them at fixed time points. A global decrease in phospholipid signal intensity is shown to occur and to be a function of time and temperature. Contrary to the global decrease, oxidized phospholipid and lysophospholipid species are found to increase within 2 h and 24 h, respectively, when mounted sections are kept at ambient room conditions. Imaging experiments reveal that degradation products increase globally across the tissue. Degradation is shown to be inhibited by cold temperatures, with sample integrity maintained up to a week after storage in -80 °C freezer under N2 atmosphere. Overall, the results demonstrate a timeline of the effects of lipid degradation specific to sectioned tissues and provide several lipid species which can serve as markers of degradation. Importantly, the timeline demonstrates oxidative sample degradation begins appearing within the normal timescale of IMS sample preparation of lipids (i.e. 1-2 h) and that long-term degradation is global. Taken together, these results strengthen the notion that standardized procedures are required for phospholipid IMS of large sample sets, or in studies where many serial sections are prepared together but analyzed over time such as in 3-D IMS reconstruction experiments.
Rapid Communications in Mass Spectrometry, Jul 31, 1996
By the incorporation of delayed extraction (DE) into matrix-assisted laser dmrptionlionization ti... more By the incorporation of delayed extraction (DE) into matrix-assisted laser dmrptionlionization time-of-flight mass spectrometry a dramatic improvement of performance with respect to sensitivity, mass resolution and mass accuracy of precursor ions up to-10 kDa has been achieved. Since DE reduces collisional in-source activation to a large extent, the rate of subsequent metastable decay is considerably reduced. Results are presented which demonstrate that under DE the loss of total post-source decay (PSD) fragment ion yield can be as large as one order of magnitude but that, in terms of sensitivity, part of this loss is balanced by a better S/N ratio which results from a significantly improved mass resolution of the PSD fragment ions (M/AM up to 1800 compared with M/ bM=200-500 under prompt extraction). While this compensatory effect is true for the middle to high mass range of PSD fragment ions, it gradually vanishes towards the low mass end of the PSD mass scale where, in the case of linear peptides some important information (immonium ions) is lost. It appears, however, that in the majority of practical PSD work, DE improves the qualty of the PSD spectra and that high energy collisional post-source activation can compensate for the occasional loss of analytical information. vated decomposition) tandem MS technique^.'^-'* The
Analytical Chemistry, Jan 9, 2004
MALDI (matrix-assisted laser desorption/ionization) imaging mass spectrometry (IMS) is a new tech... more MALDI (matrix-assisted laser desorption/ionization) imaging mass spectrometry (IMS) is a new technology that generates molecular profiles and two-dimensional ion density maps of peptide and protein signals directly from the surface of thin tissue sections. This allows specific information to be obtained on the relative abundance and spatial distribution of proteins. One important aspect of this is the opportunity to correlate these specific ion images with histological features observed by optical microscopy. To facilitate this, we have developed protocols that allow MALDI mass spectrometry imaging and optical microscopy to be performed on the same section. Key components of these protocols involve the use of conductive glass slides as sample support for the tissue sections and MS-friendly tissue staining protocols. We show the effectiveness of these with protein standards and with several types of tissue sections. Although stain-specific intensity variations occur, the overall protein pattern and spectrum quality remain consistent between stained and control tissue samples. Furthermore, imaging mass spectrometry experiments performed on stained sections showed good image quality with minimal delocalization of proteins resulting from the staining protocols.
New developments in mass spectrometry, 2021
Journal of Proteomics & Bioinformatics, Jul 1, 2008
MALDI imaging mass spectrometry (IMS) can be used to map the molecular content of surfaces. This ... more MALDI imaging mass spectrometry (IMS) can be used to map the molecular content of surfaces. This powerful analytical approach has primarily been used to study the composition and spatial distribution of molecules within tissue sections. Methodologies for the analysis of endogenous compounds such as lipids, peptides and proteins as well as administered pharmaceutics have been developed to better understand the molecular aspects of normal organ functioning, and development as well as the progression of diseases.
Wiley-VCH Verlag GmbH eBooks, Dec 18, 2007
Analytical and Bioanalytical Chemistry, Nov 9, 2014
Imaging mass spectrometry (IMS) is a technique in full expansion used in many clinical and biolog... more Imaging mass spectrometry (IMS) is a technique in full expansion used in many clinical and biological applications. A common limitation of the technology, particularly true for protein analysis, is that only the most abundant and/ or more easily ionizable molecules are typically detected. One approach to overcome this limitation is to transfer proteins contained within tissue sections onto functionalized surfaces with high spatial fidelity for IMS analysis. In this case, only proteins with an affinity for the surface will be retained whereas others will be removed. The chemical nature of the surface is therefore critical. The research work presented herein proposes a high spatial fidelity transfer method for proteins from thin tissue sections onto a nitrocellulose surface. The method employs a home-built apparatus that allows the transfer process to be performed without any direct physical contact between the section and the transfer surface while maintaining physical pressure between the surfaces to help protein migration. The performance of this system was demonstrated using mouse liver and kidney sections. Serials sections were also collected either to be stained with hematoxylin and eosin (H&E) to assess the spatial fidelity of the transfer process or to be directly analyzed as a control sample to differentiate the signals detected after transfer. IMS results showed a high spatial fidelity transfer of a subset of proteins. Some of the detected proteins were poorly observed or not observed with conventional direct tissue analysis, demonstrating an increase in detection sensitivity and specificity with the newly developed method.
PLOS ONE, Mar 26, 2015
Degarelix is a gonadrotropin-releasing hormone (GnRH) receptor (GnRHR) antagonist used in patient... more Degarelix is a gonadrotropin-releasing hormone (GnRH) receptor (GnRHR) antagonist used in patients with prostate cancer who need androgen deprivation therapy. GnRHRs have been found in extra-pituitary tissues, including prostate, which may be affected by the GnRH and GnRH analogues used in therapy. The direct effect of degarelix on human prostate cell growth was evaluated. Normal prostate myofibroblast WPMY-1 and epithelial WPE1-NA22 cells, benign prostatic hyperplasia (BPH)-1 cells, androgen-independent PC-3 and androgen-dependent LNCaP prostate cancer cells, as well as VCaP cells derived from a patient with castration-resistant prostate cancer were used. Discriminatory protein and lipid fingerprints of normal, hyperplastic, and cancer cells were generated by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). The investigated cell lines express GNRHR1 and GNRHR2 and their endogenous ligands. Degarelix treatment reduced cell viability in all prostate cell lines tested, with the exception of the PC-3 cells; this can be attributed to increased apoptosis, as indicated by increased caspase 3/7, 8 and 9 levels. WPE1-NA22, BPH-1, LNCaP, and VCaP cell viability was not affected by treatment with the GnRH agonists leuprolide and goserelin. Using MALDI MS, we detected changes in m/z signals that were robust enough to create a complete discriminatory profile induced by degarelix. Transcriptomic analysis of BPH-1 cells provided a global map of genes affected by degarelix and indicated that the biological processes affected were related to cell growth, G-coupled receptors, the mitogen-activated protein kinase (MAPK) pathway, angiogenesis and cell adhesion. Taken together, these data demonstrate that (i) the GnRH antagonist degarelix exerts a direct effect on prostate cell growth through apoptosis; (ii) MALDI MS analysis provided a basis to fingerprint degarelix-treated prostate cells; and (iii) the clusters of genes affected by degarelix suggest that this compound, in addition to its known use in the treatment of prostate cancer, may be efficacious in BPH.
PubMed, Mar 1, 2004
MALDI imaging MS allows simultaneous mapping of hundreds of peptides and proteins in thin tissue ... more MALDI imaging MS allows simultaneous mapping of hundreds of peptides and proteins in thin tissue sections with a lateral resolution of ~30-50 μm.
Thrombosis and Haemostasis, 2012
SummaryIschaemic stroke and myocardial infarction often result from the sudden rupture of an athe... more SummaryIschaemic stroke and myocardial infarction often result from the sudden rupture of an atherosclerotic plaque. The subsequent arterial thrombosis occluding the vessel lumen has been widely indicated as the crucial acute event causing peripheral tissue ischaemia. A complex cross-talk between systemic and intraplaque inflammatory mediators has been shown to regulate maturation, remodeling and final rupture of an atherosclerotic plaque. Matrix metalloproteinases (MMPs) are proteolytic enzymes (released by several cell subsets within atherosclerotic plaques), which favour atherogenesis and increase plaque vulnerability. Thus, the assessment of intraplaque levels and activity of MMP might be of pivotal relevance in the evaluation of the risk of rupture. New imaging approaches, focused on the visualisation of inflammation in the vessel wall and plaque, may emerge as tools for individualised risk assessment and prevention of events. In this review, we summarize experimental findings of the currently available invasive and noninvasive imaging techniques, used to detect the presence and activity of MMPs in atherosclerotic plaques.
Analyst, 2018
Supplemental Material Groomed latent fingermarks were prepared on ITO-coated slides, glass slides... more Supplemental Material Groomed latent fingermarks were prepared on ITO-coated slides, glass slides and porous surfaces according to published preparation methods (Ref.36). The finger was rubbed on the forehead, nose and chin several times in order to produce a sebum-rich fingermark containing common exogenous substances.
Microbial Ecology, May 16, 2019
Probiotics can ameliorate diseases of humans and wildlife, but the mechanisms remain unclear. Hos... more Probiotics can ameliorate diseases of humans and wildlife, but the mechanisms remain unclear. Host responses to interventions that change their microbiota are largely uncharacterized. We applied a consortium of four natural antifungal bacteria to the skin of endangered Sierra Nevada yellow-legged frogs, Rana sierrae, before experimental exposure to the pathogenic fungus Batrachochytrium dendrobatidis (Bd). The probiotic microbes did not persist, nor did they protect hosts, and skin peptide sampling indicated immune modulation. We characterized a novel skin defense peptide brevinin-1Ma (FLPILAGLAANLVPKLICSITKKC) that was downregulated by the probiotic treatment. Brevinin-1Ma was tested against a range of amphibian skin cultures and found to inhibit growth of fungal pathogens Bd and B. salamandrivorans, but enhanced the growth of probiotic bacteria including Janthinobacterium lividum, Chryseobacterium ureilyticum, Serratia grimesii, and Pseudomonas sp. While commonly thought of as antimicrobial peptides, here brevinin-1Ma showed promicrobial function, facilitating microbial growth. Thus, skin exposure to probiotic bacterial cultures induced a shift in skin defense peptide profiles that appeared to act as an immune response functioning to regulate the microbiome. In addition to direct microbial antagonism, probiotic-host interactions may be a critical mechanism affecting disease resistance.
Analytical Chemistry, Mar 29, 2012
A novel functional Imaging Mass Spectrometry technology is described that utilizes activity-based... more A novel functional Imaging Mass Spectrometry technology is described that utilizes activity-based probes for imaging enzyme active sites in tissue sections. We demonstrate this technology using an activity-based probe (fluorophosphate) that is specific for serine hydrolases. A dendrimer containing multiple mass tags that is attached to the activity-based probe is used to analyze the binding sites of the probe through release and measurement of the mass tags on laser irradiation. A generation 8 Poly(amido amine) dendrimer with 1024 amino groups was labeled with an azide group and then more than 900 mass tags were attached in order to achieve signal amplification of nearly three orders of magnitude. The experimental protocol first involves binding of the activitybased probe containing an alkyne group to serine hydrolases in the tissue section followed by attachment of the dendrimer labeled with mass tags to the bound probe by Click chemistry. On irradiation of the labeled tissue by the laser beam in a raster pattern, the mass tags are liberated and recorded by the mass analyzer, consequently, the ion image of the mass tag reveals the distribution of serine hydrolases in the tissue. This process was shown using rat brain and mouse embryo sections. Targeted imaging has the advantage of providing high spatial resolution and high sensitivity through the use of signal amplification chemistry with high target specificity through the use of an enzyme activity probe.
Journal of Mass Spectrometry, 2013
Imaging mass spectrometry (IMS) is an emergent and innovative approach for measuring the composit... more Imaging mass spectrometry (IMS) is an emergent and innovative approach for measuring the composition, abundance and regioselectivity of molecules within an investigated area of fixed dimension. Although providing unprecedented molecular information compared with conventional MS techniques, enhancement of protein signature by IMS is still necessary and challenging. This paper demonstrates the combination of conventional organic washes with an optimized aqueous-based buffer for tissue section preparation before matrix-assisted laser desorption/ionization (MALDI) IMS of proteins. Based on a 500 mM ammonium formate in water-acetonitrile (9:1; v/v, 0.1% trifluororacetic acid, 0.1% Triton) solution, this buffer wash has shown to significantly enhance protein signature by profiling and IMS (~fourfold) when used after organic washes (70% EtOH followed by 90% EtOH), improving the quality and number of ion images obtained from mouse kidney and a 14-day mouse fetus whole-body tissue sections, while maintaining a similar reproducibility with conventional tissue rinsing. Even if some protein losses were observed, the data mining has demonstrated that it was primarily low abundant signals and that the number of new peaks found is greater with the described procedure. The proposed buffer has thus demonstrated to be of high efficiency for tissue section preparation providing novel and complementary information for direct on-tissue MALDI analysis compared with solely conventional organic rinsing.
Thrombosis and Haemostasis, 2011
The identification and quantification of proteins and lipids is of major importance for the diagn... more The identification and quantification of proteins and lipids is of major importance for the diagnosis, prognosis and understanding of the molecular mechanisms involved in disease development. Owing to its selectivity and sensitivity, mass spectrometry has become a key technique in analytical platforms for proteomic and lipidomic investigations. Using this technique, many strategies have been developed based on unbiased or targeted approaches to highlight or monitor molecules of interest from biomatrices. Although these approaches have largely been employed in cancer research, this type of investigation has been met by a growing interest in the field of cardiovascular disorders, potentially leading to the discovery of novel biomarkers and the development
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Papers by Pierre Chaurand