Tissue storage affects lipidome profiling in comparison to in vivo microsampling approach

Exploring sample treatment strategies for untargeted metabolomics: A comparative study of solid phase microextraction (SPME) and homogenization with solid-liquid extraction (SLE) in renal tissue

BACKGROUND

The selection of the sample treatment strategy is a crucial step in the metabolomics workflow. Solid phase microextraction (SPME) is a sample processing methodology with great potential for use in untargeted metabolomics of tissue samples. However, its utilization is not as widespread as other standard protocols involving steps of tissue collection, metabolism quenching, homogenization, and extraction of metabolites by solvents. Since SPME allows us to perform all these steps in one action in tissue samples, in addition to other advantages, it is necessary to know whether this methodology produces similar or comparable metabolome and lipidome coverage and performance to classical methods.

RESULTS

SPME and homogenization with solid-liquid extraction (Homo-SLE) sample treatment methods were applied to healthy murine kidney tissue, followed by comprehensive metabolomics and lipidomics analyses. In addition, it has been tested whether freezing and storage of the tissue causes alterations in the renal metabolome and lipidome, so the analyses were performed on fresh and frozen tissue samples Lipidomics analysis revealed the exclusive presence of different structural membrane and intracellular lipids in the Homo-SLE group. Conversely, all annotated metabolites were detected in both groups. Notably, the freezing of the sample mainly causes a decrease in the levels of most lipid species and an increase in metabolites such as amino acids, purines, and pyrimidines. These alterations are principally detected in a statistically significant way by SPME methodology. Finally, the samples of both methodologies show a positive correlation in all the analyses.

SIGNIFICANCE

These results demonstrate that in SPME processing, as long as the fundamentals of non-exhaustive extraction in a pre-equilibrium kinetic regime, extraction in a tissue localized area, the chemistry of the fiber coating and non-homogenization of the tissue are taken into account, is an excellent method to use in kidney tissue metabolomics; since this methodology presents an easy-to-use, efficient, and less invasive approach that simplifies the different sample processing steps.

Recent advance on microextraction sampling technologies for bioanalysis

The contents of target substances in biological samples are usually at low concentration levels, and the matrix of biological samples is usually complex. Sample preparation is considered a very critical step in bioanalysis. At present, the utilization of microextraction sampling technology has gained considerable prevalence in the realm of biological analysis. The key developments in this field focus on the efficient microextraction media and the miniaturization and automation of adaptable sample preparation methods currently. In this review, the recent progress on the microextraction sampling technologies for bioanalysis has been introduced from point of view of the preparation of microextraction media and the microextraction sampling strategies. The advance on the microextraction media was reviewed in detail, mainly including the aptamer-functionalized materials, molecularly imprinted polymers, carbon-based materials, metal-organic frameworks, covalent organic frameworks, etc. The advance on the microextraction sampling technologies was summarized mainly based on in-vivo sampling, in-vitro sampling and microdialysis technologies. Moreover, the current challenges and perspective on the future trends of microextraction sampling technologies for bioanalysis were briefly discussed.

In vivo solid phase microextraction for therapeutic monitoring and pharmacometabolomic fingerprinting of lung during in vivo lung perfusion of FOLFOX

In vivo lung perfusion (IVLP) is a novel isolated lung technique developed to enable the local, in situ administration of high-dose chemotherapy to treat metastatic lung cancer. Combination therapy using folinic acid (FOL), 5-fluorouracil (F), and oxaliplatin (OX) (FOLFOX) is routinely employed to treat several types of solid tumours in various tissues. However, F is characterized by large interpatient variability with respect to plasma concentration, which necessitates close monitoring during treatments using of this compound. Since plasma drug concentrations often do not reflect tissue drug concentrations, it is essential to utilize sample-preparation methods specifically suited to monitoring drug levels in target organs. In this work, in vivo solid-phase microextraction (in vivo SPME) is proposed as an effective tool for quantitative therapeutic drug monitoring of FOLFOX in porcine lungs during pre-clinical IVLP and intravenous (IV) trials. The concomitant extraction of other endogenous and exogenous small molecules from the lung and their detection via liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) enabled an assessment of FOLFOX's impact on the metabolomic profile of the lung and revealed the metabolic pathways associated with the route of administration (IVLP vs. IV) and the therapy itself. This study also shows that the immediate instrumental analysis of metabolomic samples is ideal, as long-term storage at -80 °C results in changes in the metabolite content in the sample extracts.

Monitoring of age- and gender-related alterations of endocannabinoid levels in selected brain regions with the use of SPME probes

INTRODUCTION

The endocannabinoid system consists of different types of receptors, enzymes and endocannabinoids (ECs), which are involved in several physiological processes, but also play important role in the development and progression of central nervous system disorders.

OBJECTIVES

The purpose of this study was to apply precise and sensitive methodology for monitoring of four ECs, namely anandamide (AEA), 2-arachidonoyl glycerol (2-AG), N-arachidonoyl dopamine (NADA), 2-arachidonyl glyceryl ether (2-AGe) in selected brain regions of female and male rats at different stages of development (young, adult and old).

METHODS

Biocompatible solid-phase microextraction (SPME) probes were introduced into the intact (non-homogenized) brain structures for isolation of four ECs, and the extracts were subjected to LC-MS/MS analysis. Two chemometric approaches, namely hierarchical cluster analysis (HCA) and Principal Component Analysis (PCA) were applied to provide more information about the levels of 2-AG and AEA in different brain structures.

RESULTS

2-AG and AEA were extracted and could be quantified in each brain region; the level of 2-AG was significantly higher in comparison to the level of AEA. Two highly unstable ECs, NADA and 2-AGe, were captured by SPME probes from intact brain samples for the first time.

CONCLUSION

SPME probes were able to isolate highly unstable endogenous compounds from intact tissue, and provided new tools for precise analysis of the level and distribution of ECs in different brain regions. Monitoring of ECs in brain samples is important not only in physiological conditions, but also may contribute to better understanding of the functioning of the endocannabinoid system in various disorders.

Solid-phase microextraction of endogenous metabolites from intact tissue validated using a Biocrates standard reference method kit

Improved analytical methods for the metabolomic profiling of tissue samples are constantly needed. Currently, conventional sample preparation methods often involve tissue biopsy and/or homogenization, which disrupts the endogenous metabolome. In this study, solid-phase microextraction (SPME) fibers were used to monitor changes in endogenous compounds in homogenized and intact ovine lung tissue. Following SPME, a Biocrates AbsoluteIDQ assay was applied to make a downstream targeted metabolomics analysis and confirm the advantages of in vivo SPME metabolomics. The AbsoluteIDQ kit enabled the targeted analysis of over 100 metabolites via solid-liquid extraction and SPME. Statistical analysis revealed significant differences between conventional liquid extractions from homogenized tissue and SPME results for both homogenized and intact tissue samples. In addition, principal component analysis revealed separated clustering among all the three sample groups, indicating changes in the metabolome due to tissue homogenization and the chosen sample preparation method. Furthermore, clear differences in free metabolites were observed when extractions were performed on the intact and homogenized tissue using identical SPME procedures. Specifically, a direct comparison showed that 47 statistically distinct metabolites were detected between the homogenized and intact lung tissue samples (P < 0.05) using mixed-mode SPME fibers. These changes were probably due to the disruptive homogenization of the tissue. This study's findings highlight both the importance of sample preparation in tissue-based metabolomics studies and SPME's unique ability to perform minimally invasive extractions without tissue biopsy or homogenization while providing broad metabolite coverage.

Metabolomic fingerprinting of porcine lung tissue during pre-clinical prolonged ex vivo lung perfusion using in vivo SPME coupled with LC-HRMS

Normothermic ex vivo lung perfusion (NEVLP) has emerged as a modernized organ preservation technique that allows for detailed assessment of donor lung function prior to transplantation. The main goal of this study was to identify potential biomarkers of lung function and/or injury during a prolonged (19 h) NEVLP procedure using in vivo solid-phase microextraction (SPME) technology followed by liquid chromatography-high resolution mass spectrometry (LC-HRMS). The use of minimally invasive in vivo SPME fibers for repeated sampling of biological tissue permits the monitoring and evaluation of biochemical changes and alterations in the metabolomic profile of the lung. These in vivo SPME fibers were directly introduced into the lung and were also used to extract metabolites (on-site SPME) from fresh perfusate samples collected alongside lung samplings. A subsequent goal of the study was to assess the feasibility of SPME as an in vivo method in metabolomics studies, in comparison to the traditional in-lab metabolomics workflow. Several upregulated biochemical pathways involved in pro- and anti-inflammatory responses, as well as lipid metabolism, were observed during extended lung perfusion, especially between the 11th and 12th hours of the procedure, in both lung and perfusate samples. However, several unstable and/or short-lived metabolites, such as neuroprostanes, have been extracted from lung tissue in vivo using SPME fibers. On-site monitoring of the metabolomic profiles of both lung tissues through in vivo SPME and perfusate samples on site throughout the prolonged NEVLP procedure can be effectively performed using in vivo SPME technology.

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In vivo SPME monitors metabolic changes in porcine lung during 19-h NEVLP.

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On-site SPME for perfusate sampling monitors metabolite composition during NEVLP.

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SPME-LC-HRMS permits identification of potential metabolic markers of lung function.

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Stored perfusate provides less relevant metabolome information compared to on-site perfusate samples.

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In vivo SPME of the lung provides more metabolomic information than perfusate sampling.

Determination of Brain Tissue Samples Storage Conditions for Reproducible Intraoperative Lipid Profiling

Ex-vivo molecular profiling has recently emerged as a promising method for intraoperative tissue identification, especially in neurosurgery. The short-term storage of resected samples at room temperature is proposed to have negligible influence on the lipid molecular profiles. However, a detailed investigation of short-term molecular profile stability is required to implement molecular profiling in a clinic. This study evaluates the effect of storage media, temperature, and washing solution to determine conditions that provide stable and reproducible molecular profiles, with the help of ambient ionization mass spectrometry using rat cerebral cortex as model brain tissue samples. Utilizing normal saline for sample storage and washing media shows a positive effect on the reproducibility of the spectra; however, the refrigeration shows a negligible effect on the spectral similarity. Thus, it was demonstrated that up to hour-long storage in normal saline, even at room temperature, ensures the acquisition of representative molecular profiles using ambient ionization mass spectrometry.

Investigating the Potential Use of Chemical Biopsy Devices to Characterize Brain Tumor Lipidomes

The development of a fast and accurate intraoperative method that enables the differentiation and stratification of cancerous lesions is still a challenging problem in laboratory medicine. Therefore, it is important to find and optimize a simple and effective analytical method of enabling the selection of distinctive metabolites. This study aims to assess the usefulness of solid-phase microextraction (SPME) probes as a sampling method for the lipidomic analysis of brain tumors. To this end, SPME was applied to sample brain tumors immediately after excision, followed by lipidomic analysis via liquid chromatography-high resolution mass spectrometry (LC-HRMS). The results showed that long fibers were a good option for extracting analytes from an entire lesion to obtain an average lipidomic profile. Moreover, significant differences between tumors of different histological origin were observed. In-depth investigation of the glioma samples revealed that malignancy grade and isocitrate dehydrogenase (IDH) mutation status impact the lipidomic composition of the tumor, whereas 1p/19q co-deletion did not appear to alter the lipid profile. This first on-site lipidomic analysis of intact tumors proved that chemical biopsy with SPME is a promising tool for the simple and fast extraction of lipid markers in neurooncology.

In Vivo Solid-Phase Microextraction and Applications in Environmental Sciences

Solid-phase microextraction (SPME) is a well-established sample-preparation technique for environmental studies. The application of SPME has extended from the headspace extraction of volatile compounds to the capture of active components in living organisms via the direct immersion of SPME probes into the tissue (in vivo SPME). The development of biocompatible coatings and the availability of different calibration approaches enable the in vivo sampling of exogenous and endogenous compounds from the living plants and animals without the need for tissue collection. In addition, new geometries such as thin-film coatings, needle-trap devices, recession needles, coated tips, and blades have increased the sensitivity and robustness of in vivo sampling. In this paper, we detail the fundamentals of in vivo SPME, including the various extraction modes, coating geometries, calibration methods, and data analysis methods that are commonly employed. We also discuss recent applications of in vivo SPME in environmental studies and in the analysis of pollutants in plant and animal tissues, as well as in human saliva, breath, and skin analysis. As we show, in vivo SPME has tremendous potential for the targeted and untargeted screening of small molecules in living organisms for environmental monitoring applications.

Breaking Through the Barrier: Regulatory Considerations Relevant to Ambient Mass Spectrometry at the Bedside

Rapid characterization of tissue disorder using ambient mass spectrometry (MS) techniques, requiring little to no preanalytical preparations of sampled tissues, has been shown using a variety of ion sources and with many disease classes. A brief overview of ambient MS in clinical applications, the state of the art in regulatory affairs, and recommendations to facilitate adoption for use at the bedside are presented. Unique challenges in the validation of untargeted MS methods and additional safety and compliance requirements for deployment within a clinical setting are further discussed. Development of a harmonized validation strategy for ambient MS methods is emphasized.

Recent Applications of Solid Phase Microextraction Coupled to Liquid Chromatography

Solid phase microextraction (SPME) is one of the most popular sample preparation methods which can be applied to organic compounds allowing the simultaneous extraction and pre-concentration of analytes from the sample matrix. It is based on the partitioning of the analyte between the extracting phase, generally immobilized on a fiber substrate, and the matrix (water, air, etc.), and has numerous advantages such as rapidity, simplicity, low cost, ease of use and automation, and absence of toxic solvents. Fiber SPME has been widely used in combination with various analytical instrumentation even if most of the work has been done coupling the extraction technique with gas and liquid chromatography (GC and LC). This manuscript presents an overview of the recent works (from 2010 to date) of solid phase microextraction coupled to liquid chromatography (SPME-LC) relevant to analytical applications performed using commercially available fibers or lab-made fibers already developed in previous papers, and to improved instrumental systems and approaches.

Assessment of solid phase microextraction as a sample preparation tool for untargeted analysis of brain tissue using liquid chromatography-mass spectrometry

This work presents an evaluation of solid-phase microextraction (SPME) SPME in combination with liquid chromatography-high resolution mass spectrometry (LC-HRMS) as an analytical approach for untargeted brain analysis. The study included a characterization of the metabolite coverage provided by C18, mixed-mode (MM, with benzene sulfonic acid and C18 functionalities), and hydrophilic lipophilic balanced (HLB) particles as sorbents in SPME coatings after extraction from cow brain homogenate at static conditions. The effects of desorption solvent, extraction time, and chromatographic modes on the metabolite features detected were investigated. Method precision and absolute matrix effects were also assessed. Among the main findings of this work, it was observed that all three tested coating chemistries were able to provide comparable brain tissue information. HLB provided higher responses for polar metabolites; however, as these fibers were prepared in-house, higher inter-fiber relative standard deviations were also observed. C18 and HLB coatings offered similar responses with respect to lipid-related features, whereas MM and C18 provided the best results in terms of method precision. Our results also showed that the use of methanol is essential for effective desorption of non-polar metabolites. Using a reversed-phase chromatographic method, an average of 800 and 1200 brain metabolite features detected in positive and negative modes, respectively, met inter-fibre RSD values below 30% (n=4) after removal of fibre and solvent artefacts from the associated datasets. For features detected using a lipidomics method, a total of 900 and 1800 features detected using C18 fibers in positive and negative mode, respectively, met the same criteria. In terms of absolute matrix effects, the majority of the model metabolites tested showed values between 80 and 120%, which are within the acceptable range. Overall, the findings of this work lay the foundation for further optimization of parameters for SPME-LC-HRMS methods suitable for in vivo and ex vivo brain (and other tissue) untargeted studies, and support the applicability of this approach for non-destructive tissue metabolomics.

Investigation of Early Death-Induced Changes in Rat Brain by Solid Phase Microextraction via Untargeted High Resolution Mass Spectrometry: In Vivo versus Postmortem Comparative Study

Analysis of brain samples obtained postmortem remains a standard approach in neuroscience, despite often being suboptimal for inferring roles of small molecules in the pathophysiology of brain diseases. Sample collection and preservation further hinders conclusive interpretation of biomarker analysis in autopsy samples. We investigate purely death-induced changes affecting rat hippocampus in the first hour of postmortem interval (PMI) by means of untargeted liquid chromatography-mass spectrometry-based metabolomics. The unique possibility of sampling the same brain area of each animal both in vivo and postmortem was enabled by employing solid phase microextraction (SPME) probes. Four millimeter probes coated with mixed mode extraction phase were used to sample awake, freely roaming animals, with 2 more sampling events performed after death. Significant changes in brain neurochemistry were found to occur as soon as 30 min after death, further progressing with increasing PMI, evidenced by relative changes in levels of metabolites and lipids. These included species from several distinct groups, which can be classified as engaged in energy metabolism-related processes, signal transduction, neurotransmission, or inflammatory response. Additionally, we perform thorough analysis of interindividual variability in response to death, which provides insights into how this aspect can obscure conclusions drawn from an untargeted study at single metabolite and pathway level. The results suggest high demand for systematic studies examining the PMI time course with in vivo sampling as a starting point to eliminate artifacts in the form of neurochemical changes assumed to occur in vivo.

A Review of Efforts to Improve Lipid Stability during Sample Preparation and Standardization Efforts to Ensure Accuracy in the Reporting of Lipid Measurements

Lipidomics is a rapidly growing field, fueled by developments in analytical instrumentation and bioinformatics. To date, most researchers and industries have employed their own lipidomics workflows without a consensus on best practices. Without a community-wide consensus on best practices for the prevention of lipid degradation and transformations through sample collection and analysis, it is difficult to assess the quality of lipidomics data and hence trust results. Clinical studies often rely on samples being stored for weeks or months until they are analyzed, but inappropriate sampling techniques, storage temperatures, and analytical protocols can result in the degradation of complex lipids and the generation of oxidized or hydrolyzed metabolite artifacts. While best practices for lipid stability are sample dependent, it is generally recommended that strategies during sample preparation capable of quenching enzymatic activity and preventing oxidation should be considered. In addition, after sample preparation, lipid extracts should be stored in organic solvents with antioxidants at -20 °C or lower in an airtight container without exposure to light or oxygen. This will reduce or eliminate sublimation, and chemically and physically induced molecular transformations such as oxidation, enzymatic transformation, and photon/heat-induced degradation. This review explores the available literature on lipid stability, with a particular focus on human health and/or clinical lipidomic applications. Specifically, this includes a description of known mechanisms of lipid degradation, strategies, and considerations for lipid storage, as well as current efforts for standardization and quality insurance of protocols.

Recent Advances in In Vivo SPME Sampling

In vivo solid-phase microextraction (SPME) has been recently proposed for the extraction, clean-up and preconcentration of analytes of biological and clinical concern. Bioanalysis can be performed by sampling exo- or endogenous compounds directly in living organisms with minimum invasiveness. In this context, innovative and miniaturized devices characterized by both commercial and lab-made coatings for in vivo SPME tissue sampling have been proposed, thus assessing the feasibility of this technique for biomarker discovery, metabolomics studies or for evaluating the environmental conditions to which organisms can be exposed. Finally, the possibility of directly interfacing SPME to mass spectrometers represents a valuable tool for the rapid quali- and quantitative analysis of complex matrices. This review article provides a survey of in vivo SPME applications focusing on the extraction of tissues, cells and simple organisms. This survey will attempt to cover the state-of- the-art from 2014 up to 2019.

Optimization of XCMS parameters for LC-MS metabolomics: an assessment of automated versus manual tuning and its effect on the final results

INTRODUCTION

Several software packages containing diverse algorithms are available for processing Liquid Chromatography-Mass Spectrometry (LC-MS) chromatographic data and within these deconvolution packages different parameters settings can lead to different outcomes. XCMS is the most widely used peak picking and deconvolution software for metabolomics, but the parameter selection can be hard for inexpert users. To solve this issue, the automatic optimization tools such as Isotopologue Parameters Optimization (IPO) can be extremely helpful.

OBJECTIVES

To evaluate the suitability of IPO as a tool for XCMS parameters optimization and compare the results with those manually obtained by an exhaustive examination of the LC-MS characteristics and performance.

METHODS

Raw HPLC-TOF-MS data from two types of biological samples (liver and plasma) analysed in both positive and negative electrospray ionization modes from three groups of piglets were processed with XCMS using parameters optimized following two different approaches: IPO and Manual. The outcomes were compared to determine the advantages and disadvantages of using each method.

RESULTS

IPO processing produced the higher number of repeatable (%RSD < 20) and significant features for all data sets and allowed the different piglet groups to be distinguished. Nevertheless, on multivariate level, similar clustering results were obtained by Principal Component Analysis (PCA) when applied to IPO and manual matrices.

CONCLUSION

IPO is a useful optimization tool that helps in choosing the appropriate parameters. It works well on data with a good LC-MS performance but the lack of such adequate data can result in unrealistic parameter settings, which might require further investigation and manual tuning. On the contrary, manual selection criteria requires deeper knowledge on LC-MS, programming language and XCMS parameter interpretation, but allows a better fine-tuning of the parameters, and thus more robust deconvolution.

In vivo solid-phase microextraction sampling combined with metabolomics and toxicological studies for the non-lethal monitoring of the exposome in fish tissue

Various environmental studies have employed the biomonitoring of fish in their aquatic ecosystems in order to identify potential metabolic responses to the exposome. In this study, we applied in vivo solid-phase microextraction (SPME) to perform non-lethal sampling on the muscle tissue of living fish to extract toxicants and various endogenous metabolites. Sixty white suckers (Catastomus commersonii) were sampled from sites upstream, adjacent, and downstream from the oil sands development region of the Athabasca River (Alberta, Canada) in order to track their biochemical responses to potential contaminants. In vivo SPME sampling facilitated the extraction of a wide range of endogenous metabolites, mainly related to lipid metabolism. The obtained results revealed significant changes in the levels of numerous metabolites, including eicosanoids, linoleic acids, and fat-soluble vitamins, in fish sampled in different areas of the river, thus demonstrating SPME's applicability for the direct monitoring of exposure to different environmental toxicants. In addition, several classes of toxins, including petroleum-related compounds, that can cause serious physiological impairment were tentatively identified in the extracts. In vivo SPME, combined with the analysis of contaminants and endogenous metabolites, provided important information about the exposome; as such, this approach represents a potentially powerful and non-lethal tool for identifying the mechanisms that produce altered metabolic pathways in response to the mixtures of different environmental pollutants.

Solid-phase microextraction: An appealing alternative for the determination of endogenous substances - A review

The determination of endogenous substances is of great significance for obtaining important biotic information such as biological components, metabolic pathways and disease biomarkers in different living organisms (e.g. plants, insects, animals and humans). However, due to the complex matrix and the trace concentrations of target analytes, the sample preparation procedure is an essential step before the analytes of interest are introduced into a detection instrument. Solid-phase microextraction (SPME), an emerging sample preparation technique that integrates sampling, extraction, concentration, and sample introduction into one step, has gained wide acceptance in various research fields, including in the determination of endogenous compounds. In this review, recent developments and applications of SPME for the determination of endogenous substances over the past five years are summarized. Several aspects, including the design of SPME devices (sampling configuration and coating), applications (in vitro and in vivo sampling), and coupling with emerging instruments (comprehensive two-dimensional gas chromatography (GC × GC), ambient mass spectrometry (AMS) and surface enhanced Raman scattering (SERS)) are involved. Finally, the challenges and opportunities of SPME methods in endogenous substances analysis are also discussed.