Sample Preparation for Metabolite Detection in Mass Spectrometry Imaging.

Metabolites reflect the biological state of cells and tissue, and metabolomics is therefore a field of high interest both to understand normal physiological functions and disease development. When studying heterogeneous tissue samples, mass spectrometry imaging (MSI) is a valuable tool as it conserves the spatial distribution of analytes on tissue sections. A large proportion of metabolites are, however, small and polar, making them vulnerable to delocalizing through diffusion during sample preparation. Here we present a sample preparation method optimized to limit diffusion and delocalization of small polar metabolites in fresh frozen tissue sections. This sample preparation protocol includes cryosectioning, vacuum frozen storage, and matrix application. The methods described were primely developed for matrix-assisted laser desorption/ionization (MALDI) MSI, but the protocol describing cryosectioning and vacuum freezing storage can also be applied before desorption electrospray ionization (DESI) MSI. Our vacuum drying and vacuum packing approach offers a particular advantage to limit delocalization and safe storage.

Visualization of Small Intact Proteins in Breast Cancer FFPE Tissue.

Molecular visualization of metabolites, lipids, and proteins by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is becoming an in-demand analytical approach to aid the histopathological analysis of breast cancer. Particularly, proteins seem to play a role in cancer progression, and specific proteins are currently used in the clinic for staging. Formalin-fixed paraffin-embedded (FFPE) tissues are ideal for correlating the molecular markers with clinical outcomes due to their long-term storage. So far, to obtain proteomic information by MSI from this kind of tissue, antigen retrieval and tryptic digestion steps are required. In this chapter, we present a protocol to spatially detect small proteins in tumor and necrotic regions of patient-derived breast cancer xenograft FFPE tissues without employing any on-tissue digestion. This protocol can be used for other kinds of FFPE tissue following specific optimization of the sample preparation phases.

Binding Modes of a Cytotoxic Dinuclear Copper(II) Complex with Phosphate Ligands Probed by Vibrational Photodissociation Ion Spectroscopy.

The dinuclear copper complex bearing a 2,7-disubstituted-1,8-naphthalenediol ligand, [(HtomMe){Cu(OAc)}2](OAc), a potential anticancer drug able to bind to two neighboring phosphates in the DNA backbone, is endowed with stronger cytotoxic effects and inhibition ability of DNA synthesis in human cancer cells as compared to cisplatin. In this study, the intrinsic binding ability of the charged complex [(HtomMe){Cu(OAc)}2]+ is investigated with representative phosphate diester ligands with growing chemical complexity, ranging from simple inorganic phosphate up to mononucleotides. An integrated method based on high-resolution mass spectrometry (MS), tandem MS, and infrared multiple photon dissociation (IRMPD) spectroscopy in the 600-1800 cm-1 spectral range, backed by quantum chemical calculations, has been used to characterize complexes formed in solution and delivered as bare species by electrospray ionization. The structural features revealed by IRMPD spectroscopy have been interpreted by comparison with linear IR spectra of the lowest-energy structures, revealing diagnostic signatures of binding modes of the dinuclear copper(II) complex with phosphate groups, whereas the possible competitive interaction with the nucleobase is silenced in the gas phase. This result points to the prevailing interaction of [(HtomMe){Cu(OAc)}2]+ with phosphate diesters and mononucleotides as a conceivable contribution to the observed anticancer activity.

An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue.

MALDI MS imaging (MSI) is a powerful analytical tool for spatial peptide detection in heterogeneous tissues. Proper sample preparation is crucial to achieve high quality, reproducible measurements. Here we developed an optimized protocol for spatially resolved proteolytic peptide detection with MALDI time-of-flight MSI of fresh frozen prostate tissue sections. The parameters tested included four different tissue washes, four methods of protein denaturation, four methods of trypsin digestion (different trypsin densities, sprayers, and incubation times), and five matrix deposition methods (different sprayers, settings, and matrix concentrations). Evaluation criteria were the number of detected and excluded peaks, percentage of high mass peaks, signal-to-noise ratio, spatial localization, and average intensities of identified peptides, all of which were integrated into a weighted quality evaluation scoring system. Based on these scores, the optimized protocol included an ice-cold EtOH+H2 O wash, a 5 min heating step at 95°C, tryptic digestion incubated for 17h at 37°C and CHCA matrix deposited at a final amount of 1.8 µg/mm2 . Including a heat-induced protein denaturation step after tissue wash is a new methodological approach that could be useful also for other tissue types. This optimized protocol for spatial peptide detection using MALDI MSI facilitates future biomarker discovery in prostate cancer and may be useful in studies of other tissue types.

Unravel the Local Complexity of Biological Environments by MALDI Mass Spectrometry Imaging.

Classic metabolomic methods have proven to be very useful to study functional biology and variation in the chemical composition of different tissues. However, they do not provide any information in terms of spatial localization within fine structures. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) does and reaches at best a spatial resolution of 0.25 µm depending on the laser setup, making it a very powerful tool to analyze the local complexity of biological samples at the cellular level. Here, we intend to give an overview of the diversity of the molecules and localizations analyzed using this method as well as to update on the latest adaptations made to circumvent the complexity of samples. MALDI MSI has been widely used in medical sciences and is now developing in research areas as diverse as entomology, microbiology, plant biology, and plant-microbe interactions, the rhizobia symbiosis being the most exhaustively described so far. Those are the fields of interest on which we will focus to demonstrate MALDI MSI strengths in characterizing the spatial distributions of metabolites, lipids, and peptides in relation to biological questions.

Reproducible Lipid Alterations in Patient-Derived Breast Cancer Xenograft FFPE Tissue Identified with MALDI MSI for Pre-Clinical and Clinical Application.

The association between lipid metabolism and long-term outcomes is relevant for tumor diagnosis and therapy. Archival material such as formalin-fixed and paraffin embedded (FFPE) tissues is a highly valuable resource for this aim as it is linked to long-term clinical follow-up. Therefore, there is a need to develop robust methodologies able to detect lipids in FFPE material and correlate them with clinical outcomes. In this work, lipidic alterations were investigated in patient-derived xenograft of breast cancer by using a matrix-assisted laser desorption ionization mass spectrometry (MALDI MSI) based workflow that included antigen retrieval as a sample preparation step. We evaluated technical reproducibility, spatial metabolic differentiation within tissue compartments, and treatment response induced by a glutaminase inhibitor (CB-839). This protocol shows a good inter-day robustness (CV = 26 ± 12%). Several lipids could reliably distinguish necrotic and tumor regions across the technical replicates. Moreover, this protocol identified distinct alterations in the tissue lipidome of xenograft treated with glutaminase inhibitors. In conclusion, lipidic alterations in FFPE tissue of breast cancer xenograft observed in this study are a step-forward to a robust and reproducible MALDI-MSI based workflow for pre-clinical and clinical applications.

Implementing Complementary Approaches to Shape the Mechanism of α-Synuclein Oligomerization as a Model of Amyloid Aggregation.

The aggregation of proteins into amyloid fibers is linked to more than forty still incurable cellular and neurodegenerative diseases such as Parkinson's disease (PD), multiple system atrophy, Alzheimer's disease and type 2 diabetes, among others. The process of amyloid formation is a main feature of cell degeneration and disease pathogenesis. Despite being methodologically challenging, a complete understanding of the molecular mechanism of aggregation, especially in the early stages, is essential to find new biological targets for innovative therapies. Here, we reviewed selected examples on α-syn showing how complementary approaches, which employ different biophysical techniques and models, can better deal with a comprehensive study of amyloid aggregation. In addition to the monomer aggregation and conformational transition hypothesis, we reported new emerging theories regarding the self-aggregation of α-syn, such as the alpha-helix rich tetramer hypothesis, whose destabilization induce monomer aggregation; and the liquid-liquid phase separation hypothesis, which considers a phase separation of α-syn into liquid droplets as a primary event towards the evolution to aggregates. The final aim of this review is to show how multimodal methodologies provide a complete portrait of α-syn oligomerization and can be successfully extended to other protein aggregation diseases.

Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry.

Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.

Spatial evaluation of long-term metabolic changes induced by cisplatin nephrotoxicity.

Cisplatin is a widely used chemotherapeutic agent. However, it is causing nephrotoxic side effects including a reduced glomerular filtration rate and acute kidney injury. Although kidneys can recover to an extent from the treatment, long-term damage is possible. While a lot of research is focusing on short-term effects, little is known about adverse metabolic effects in the process of recovery. In this study, male Han Wistar rats were dosed with a single intraperitoneal injection of 3 mg/kg cisplatin. Urine and kidney samples were harvested 3, 8 and 26 days after administration. Tubular injury was demonstrated through urinary biomarkers. Complementing this, mass spectrometry imaging gives insight on molecular alterations on a spatial level, thus making it well suited to analyze short- and long-term disturbances. Various metabolic pathways seem to be affected, as changes in a wide range of metabolites were observed between treated and control animals. Besides previously reported early changes in kidney metabolism, unprecedented long-term effects were detected including deviation in nucleotides, antioxidants, and phospholipids.

Glioblastoma multiforme: Metabolic differences to peritumoral tissue and IDH-mutated gliomas revealed by mass spectrometry imaging.

Glioblastoma multiforme (GBM) is the most common malignant primary brain tumor. High infiltration rates and poor therapy responses make it the deadliest glioma. The tumor metabolism is known to differ from normal one and is influenced through various factors which can lead to longer survival. Metabolites are small molecules (< 1500 Da) that display the metabolic pathways in the tissue. To determine the metabolic alterations between tumor and peritumoral tissue in human GBMs, mass spectrometry imaging (MSI) was performed on thin sections from 25 resected tumors. In addition, the GBMs were compared with six gliomas harboring a mutation in the isocitrate dehydrogenase (IDH1) gene (IDH1). With this technique, a manifold of analytes can be easily visualized on a single tissue section. Metabolites were annotated based on their accurate mass using high resolution MSI. Differences in their mean intensities in the tumor and peritumoral areas were statistically evaluated and abundances were visualized on the tissue. Enhanced levels of the antioxidants ascorbic acid, taurine, and glutathione in tumor areas suggest protective effects on the tumor. Increased levels of purine and pyrimidine metabolism compounds in GBM areas indicate the high energy demand. In accordance with these results, enhanced abundances of lactate and glutamine were detected. Moreover, decreased abundance of N-acetylaspartate, a marker for neuronal health, was measured in tumor areas. Obtained metabolic information could potentially support and personalize therapeutic approaches, hence emphasizing the suitability of MSI for GBM research.

Hexosamine pathway inhibition overcomes pancreatic cancer resistance to gemcitabine through unfolded protein response and EGFR-Akt pathway modulation.

Different evidence has indicated metabolic rewiring as a necessity for pancreatic cancer (PC) growth, invasion, and chemotherapy resistance. A relevant role has been assigned to glucose metabolism. In particular, an enhanced flux through the Hexosamine Biosynthetic Pathway (HBP) has been tightly linked to PC development. Here, we show that enhancement of the HBP, through the upregulation of the enzyme Phosphoacetylglucosamine Mutase 3 (PGM3), is associated with the onset of gemcitabine (GEM) resistance in PC. Indeed, mRNA profiles of GEM sensitive and resistant patient-derived tumor xenografts (PDXs) indicate that PGM3 expression is specifically increased in GEM-resistant PDXs. Of note, PGM3 results also overexpressed in human PC tissues as compared to paired adjacent normal tissues and its higher expression in PC patients is associated with worse median overall survival (OS). Strikingly, genetic or pharmacological PGM3 inhibition reduces PC cell growth, migration, invasion, in vivo tumor growth and enhances GEM sensitivity. Thus, combined treatment between a specific inhibitor of PGM3, named FR054, and GEM results in a potent reduction of xenograft tumor growth without any obvious side effects in normal tissues. Mechanistically, PGM3 inhibition, reducing protein glycosylation, causes a sustained Unfolded Protein Response (UPR), a significant attenuation of the pro-tumorigenic Epidermal Growth Factor Receptor (EGFR)-Akt axis, and finally cell death. In conclusion this study identifies the HBP as a metabolic pathway involved in GEM resistance and provides a strong rationale for a PC therapy addressing the combined treatment with the PGM3 inhibitor and GEM.

Mass spectrometry imaging reveals lipid upregulation and bile acid changes indicating amitriptyline induced steatosis in a rat model.

As a consequence of the detoxification process, drugs and drug related metabolites can accumulate in the liver, resulting in drug induced liver injury (DILI), which is the major cause for dose limitation. Amitriptyline, a commonly used tricyclic anti-depressant, is known to cause DILI. The mechanism of Amitriptyline induced liver injury is not yet completely understood. However, as it undergoes extensive hepatic metabolism, unraveling the molecular changes in the liver upon Amitriptyline treatment can help understand Amitriptyline's mode of toxicity. In this study, Amitriptyline treated male rat liver tissue was analyzed using Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging (MALDI-MSI) to investigate the spatial abundances of Amitriptyline, lipids, and bile acids. The metabolism of Amitriptyline in liver tissue was successfully demonstrated, as the spatial distribution of Amitriptyline and its metabolites localize throughout treatment group liver samples. Several lipids appear upregulated, from which nine were identified as distinct phosphatidylcholine (PC) species. The detected bile acids were found to be lower in Amitriptyline treatment group. The combined results from histological findings, Oil Red O staining, and lipid zonation by MSI revealed lipid upregulation in the periportal area indicating drug induced macrovesicular steatosis (DIS).

Immersion by rotation-based application of the matrix for fast and reproducible sample preparations and robust results in mass spectrometry imaging.

Automated matrix deposition for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is crucial for producing reproducible analyte ion signals. Here we report an innovative method employing an automated immersion apparatus, which enables a robust matrix deposition within 5 minutes and with scalable throughput by using MAPS matrix and non-polar solvents. MSI results received from mouse heart and rat brain tissues were qualitatively similar to those from nozzle sprayed samples with respect to peak number and quality of the ion images. Overall, the immersion-method enables a fast and careful matrix deposition and has the future potential for implementation in clinical tissue diagnostics.

An integrated approach to study novel properties of a MALDI matrix (4-maleicanhydridoproton sponge) for MS imaging analyses.

The chemical properties accounting for the operation of a valuable matrix used in matrix-assisted laser desorption ionization (MALDI) to perform mass spectrometry imaging (MSI), namely 3-(4,5-bis(dimethylamino)napthalen-1-yl)furan-2,5-dione (4-maleicanhydridoproton sponge, MAPS), have been elucidated also by comparison with the parent molecule 1,8-bis(dimethylamino) naphthalene (so-called proton sponge, PS). Both compounds present the bis(dimethylamino) groups, apt to efficiently trap a proton imparting positive charge. Only MAPS, though, owns the maleicanhydrido function acting as electrophile and yielding covalently bound adducts with a variety of analytes. In this way, MAPS performs as "carrier" for the analyte (A) of interest, at the same time minimizing the presence of useless, background ions. The covalent character of the adducts, [MAPS+H + A]+, is testified by their collision-induced dissociation pattern, quite distinct from the one displayed by [PS + H]+, while PS does not form any [PS + H + A]+, thus confirming the key role of the maleicanhydrido functionality of MAPS. Vibrational spectroscopy of [MAPS+H + A]+ adducts (A = H2O, NH3) provided further structural evidence. The presence of a mobile proton on A was found to be a requisite for adduct formation by electrospray ionization of acetonitrile solutions, pointing to a possible role of MAPS in discriminating competing analytes based on molecular features. The performance of MAPS has been verified in MALDI-MSI of Atropa belladonna berries, exploiting MAPS binding to atropine. Graphical abstract ᅟ.

Conjugated Polymers as a New Class of Dual-Mode Matrices for MALDI Mass Spectrometry and Imaging.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) and MALDI MS imaging are ubiquitous analytical methods in medical, pharmaceutical, biological, and environmental research. Currently, there is a strong interest in the investigation of low molecular weight compounds (LMWCs), especially to trace and understand metabolic pathways, requiring the development of new matrix systems that have favorable optical properties and a high ionization efficiency and that are MALDI silent in the LMWC area. In this paper, five conjugated polymers, poly{[ N, N'-bis(2-octyldodecyl)-naphtalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]- alt-5,5'(2,2'-bithiophene)} (PNDI(T2)), poly(3-dodecylthiophene-2,5-diyl) (P3DDT), poly{[2,3-bis(3-octyloxyphenyl)quinoxaline-5,8-diyl]- alt-(thiophene-2,5-diyl)} (PTQ1), poly{[ N, N'-bis(2-octyldodecyl)-isoindigo-5,5'-diyl] -alt-5,5'(2,2'-bithiophene)} (PII(T2)), and poly(9,9-di- n-octylfluorenyl-2,7-diyl) (P9OFl) are investigated as matrices. The polymers have a strong optical absorption, are solution processable, and can be coated into thin films, allowing a vast reduction in the amount of matrix used. All investigated polymers function as matrices in both positive and negative mode MALDI, classifying them as rare dual-mode matrices, and show a very good analyte ionization ability in both modes. PNDI(T2), P3DDT, PTQ1, and PII(T2) are MALDI silent in the full measurement range (> m/ z = 150k), except at high laser intensities. In MALDI MS experiments of single analytes and a complex biological sample, the performance of the polymers was found to be as good as two commonly used matrices (2,5-DHB for positive and 9AA for negative mode measurements). The detection limit of two standard analytes was determined as being below 164 pmol for reserpine and below 245 pmol for cholic acid. Additionally P3DDT was used successfully in first MALDI MS imaging experiments allowing the visualization of the tissue morphology of rat brain sections.

Co-encapsulation of amyloglucosidase with starch and Saccharomyces cerevisiae as basis for a long-lasting CO2 release.

CO2 is known as a major attractant for many arthropod pests which can be exploited for pest control within novel attract-and-kill strategies. This study reports on the development of a slow-release system for CO2 based on calcium alginate beads containing granular corn starch, amyloglucosidase and Saccharomyces cerevisiae. Our aim was to evaluate the conditions which influence the CO2 release and to clarify the biochemical reactions taking place within the beads. The amyloglucosidase was immobilized with a high encapsulation efficiency of 87% in Ca-alginate beads supplemented with corn starch and S. cerevisiae biomass. The CO2 release from the beads was shown to be significantly affected by the concentration of amyloglucosidase and corn starch within the beads as well as by the incubation temperature. Beads prepared with 0.1 amyloglucosidase units/g matrix solution led to a long-lasting CO2 emission at temperatures between 6 and 25 °C. Starch degradation data correlated well with the CO2 release from beads during incubation and scanning electron microscopy micrographs visualized the degradation of corn starch granules by the co-encapsulated amyloglucosidase. By implementing MALDI-ToF mass spectrometry imaging for the analysis of Ca-alginate beads, we verified that the encapsulated amyloglucosidase converts starch into glucose which is immediately consumed by S. cerevisiae cells. When applied into the soil, the beads increased the CO2 concentration in soil significantly. Finally, we demonstrated that dried beads showed a CO2 production in soil comparable to the moist beads. The long-lasting CO2-releasing beads will pave the way towards novel attract-and-kill strategies in pest control.

The influence of a modified lipopolysaccharide O-antigen on the biosynthesis of xanthan in Xanthomonas campestris pv. campestris B100.

BACKGROUND: The exopolysaccharide xanthan is a natural product which is extensively used in industry. It is a thickening agent in many fields, from oil recovery to the food sector. Xanthan is produced by the Gram negative bacterium Xanthomonas campestris pv. campestris (Xcc). We analyzed the lipopolysaccharide (LPS) of three mutant strains of the Xcc wild type B100 to distinguish if the xanthan production can be increased when LPS biosynthesis is affected. RESULTS: The Xcc B100 O-antigen (OA) is composed of a linear main chain of rhamnose residues with N-acetylfucosamine (FucNAc) side branches at every second rhamnose. It is the major LPS constituent. The O-antigen was missing completely in the mutant strain H21012 (deficient in wxcB), since neither rhamnose nor FucNAc could be detected as part of the LPS by MALDI-TOF-MS, and only a slight amount of rhamnose and no FucNAc was found by GC analysis. The LPS of two other mutants was analyzed, Xcc H28110 (deficient in wxcK) and H20110 (wxcN). In both of them no FucNAc could be detected in the LPS fraction, while the rhamnose moieties were more abundant than in wild type LPS. The measurements were carried out by GC and confirmed by MALDI-TOF-MS analyses that indicated an altered OA in which the branches are missing, while the rhamnan main chain seemed longer than in the wild type. Quantification of xanthan confirmed our hypothesis that a missing OA can lead to an increased production of the extracellular polysaccharide. About 6.3 g xanthan per g biomass were produced by the Xcc mutant H21012 (wxcB), as compared to the wild type production of approximately 5 g xanthan per g biomass. In the two mutant strains with modified OA however, Xcc H28110 (wxcK) and Xcc H20110 (wxcN), the xanthan production of 5.5 g and 5.3 g, respectively, was not significantly increased. CONCLUSIONS: Mutations affecting LPS biosynthesis can be beneficial for the production of the extracellular polysaccharide xanthan. However, only complete inhibition of the OA resulted in increased xanthan production. The inhibition of the FucNAc side branches did not lead to increased production, but provoked a novel LPS phenotype. The data suggests an elongation of the linear rhamnan main chain of the LPS OA in both the Xcc H28110 (wxcK) and Xcc H20110 (wxcN) mutant strains.

Rapid incorporation of glucosinolates as a strategy used by a herbivore to prevent activation by myrosinases.

Various plants have a binary defence system that consists of a substrate and a glucosidase, which is activated upon tissue disruption thereby forming reactive hydrolysis products. Insects feeding on such plants have to overcome this binary defence system or prevent the activation. In this study, we investigated the strategy used by a herbivore to deal with such binary defence. We studied, how the larvae of the sawfly Athalia rosae (Hymenoptera: Tenthredinidae) circumvent the activation of glucosinolates by myrosinase enzymes, which are found in their Brassicaceae host plants. Myrosinase activities were low in the front part of the larval gut but activities increased over the gut passage. In contrast, the glucosinolates were only highly concentrated in the first gut part and were rapidly incorporated into the haemolymph before the food reached the second half of the gut. Thus, the uptake and concentration of glucosinolates, i.e., sequestration, must occur in the front part of the gut. Using Matrix Assisted Laser Desorption Ionization-Mass Spectrometry Imaging (MALDI-MSI), we could demonstrate that the incorporated glucosinolate sinalbin circulates in the haemolymph where it accumulates around the Malpighian tubules. This study highlights the pivotal role of the gut of an adapted herbivore as a regulatory functional organ to cope with plant toxins. MALDI-MSI turned out as a highly useful technique to visualise glucosinolates in a herbivore, which has to deal with plants exhibiting a binary defence system, and may be applied to follow the fate of plant metabolites in other insect species in the future.