Performing efficient sample preparation with hard tumor tissue: Precellys® bead-beating homogenizer solution

Effects of glycation end-products on the dental pulp in patients with type 2 diabetes

AIM

This ex vivo study aimed to compare protein expression of advanced glycation end-products (AGE) and receptor (RAGE), and the levels of selected genes associated with inflammation and collagen within dental pulp tissue from patients with type 2 (T2D) diabetes and non-T2D.

METHODOLOGY

Noncarious extracted permanent molar teeth from patients with well-controlled T2D (n = 19) and non-T2D (controls) (n = 19) were collected and compared. The coronal pulp was examined using immunohistochemistry (IHC) (n = 10 per group) for anti-AGE and anti-RAGE. Quantitative PCR (n = 9 per group) was used to analyse the gene expression levels of NFKB, S100A12 and COLIA1. Data analyses were performed between the groups using GraphPad Prism using Pearson correlation, Shapiro-Wilk and Mann-Whitney U-tests, and multiple regression using SPSS.

RESULTS

AGEs were distributed diffusely throughout the pulp extracellular matrix associated with collagen fibres and were present on several cell types. RAGE was expressed at the pulp-dentine interface and was observed on odontoblasts, immune cells, endothelial cells and fibroblasts. Semi-quantitative analysis of IHC samples showed significantly increased expression of AGE (p < .0001) and RAGE (p = .02) in T2D samples compared with controls. The expression of NFKB (p < .0001), S100A12 (p < .0001) and COLIA1 (p = .01) genes were significantly higher in the T2D pulp, and multivariate logistic regression analysis showed that these findings were not affected by age.

CONCLUSION

T2D may exert a similar glycation response in the dental pulp to other body sites. This could occur through activation of NF-κB pathways with a concomitant increase in genes associated with inflammation and collagen.

Evaluation of Lipid Extraction Protocols for Untargeted Analysis of Mouse Tissue Lipidome

Lipidomics refers to the full characterization of lipids present within a cell, tissue, organism, or biological system. One of the bottlenecks affecting reliable lipidomic analysis is the extraction of lipids from biological samples. An ideal extraction method should have a maximum lipid recovery and the ability to extract a broad range of lipid classes with acceptable reproducibility. The most common lipid extraction relies on either protein precipitation (monophasic methods) or liquid-liquid partitioning (bi- or triphasic methods). In this study, three monophasic extraction systems, isopropanol (IPA), MeOH/MTBE/CHCl3 (MMC), and EtOAc/EtOH (EE), alongside three biphasic extraction methods, Folch, butanol/MeOH/heptane/EtOAc (BUME), and MeOH/MTBE (MTBE), were evaluated for their performance in characterization of the mouse lipidome of six different tissue types, including pancreas, spleen, liver, brain, small intestine, and plasma. Sixteen lipid classes were investigated in this study using reversed-phase liquid chromatography/mass spectrometry. Results showed that all extraction methods had comparable recoveries for all tested lipid classes except lysophosphatidylcholines, lysophosphatidylethanolamines, acyl carnitines, sphingomyelines, and sphingosines. The recoveries of these classes were significantly lower with the MTBE method, which could be compensated by the addition of stable isotope-labeled internal standards prior to lipid extraction. Moreover, IPA and EE methods showed poor reproducibility in extracting lipids from most tested tissues. In general, Folch is the optimum method in terms of efficacy and reproducibility for extracting mouse pancreas, spleen, brain, and plasma. However, MMC and BUME methods are more favored when extracting mouse liver or intestine.

Effects of Different Storage Conditions on Lipid Stability in Mice Tissue Homogenates

Lipids are biomolecules involved in numerous (patho-)physiological processes and their elucidation in tissue samples is of particular interest. However, tissue analysis goes hand in hand with many challenges and the influence of pre-analytical factors can intensively change lipid concentrations ex vivo, compromising the results of the whole research project. Here, we study the influence of pre-analytical factors on lipid profiles during the processing of homogenized tissues. Homogenates from four different mice tissues (liver, kidney, heart, spleen) were stored at room temperature as well as in ice water for up to 120 min and analyzed via ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS). Lipid class ratios were calculated since their suitability as indicators for sample stability has been previously illustrated. Only approx. 40% of lipid class ratios were unchanged after 35 min, which was further reduced to 25% after 120 min during storage at room temperature. In contrast, lipids in tissue homogenates were generally stable when samples were kept in ice water, as more than 90% of investigated lipid class ratios remained unchanged after 35 min. Ultimately, swift processing of tissue homogenates under cooled conditions represents a viable option for lipid analysis and pre-analytical factors require more attention to achieve reliable results.

Bottom-Up Proteomics: Advancements in Sample Preparation

Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC–MS/MS analysis, and data analysis. LC–MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, it is prone to errors and has low reproducibility and throughput. In-solution digestion and filter-aided sample preparation are the typical and widely used methods. In the past decade, novel methods to improve and facilitate the entire sample preparation process or integrate sample preparation and fractionation have been reported to reduce time, increase throughput, and improve reproducibility. In this review, we have outlined the current methods used for sample preparation in proteomics, including on-membrane digestion, bead-based digestion, immobilized enzymatic digestion, and suspension trapping. Additionally, we have summarized and discussed current devices and methods for integrating different steps of sample preparation and peptide fractionation.

Accurate Lipid Quantification of Tissue Homogenates Requires Suitable Sample Concentration, Solvent Composition, and Homogenization Procedure-A Case Study in Murine Liver

Lipidomics aim to quantify lipid species in all kinds of samples, including tissues. To subject a fixed amount of sample to various workflows, tissue homogenates were frequently prepared at defined concentrations in water or by addition of organic solvents. Here, we investigated this first step of tissue lipidomics by quantitative flow injection analysis coupled to Fourier-Transform mass spectrometry (FTMS). The influence of sample concentration, solvent composition, and homogenization procedure on the recovery of lipids was studied in murine liver. Liver homogenates were prepared either by grinding tissue in liquid nitrogen or by bead-based homogenization. Ground samples were dissolved at different concentrations in water, methanol, and water/methanol = 1/1 (v/v). Here, lipid recovery depends on solvent composition and sample concentration. The recovery of nonpolar lipid classes, including triglycerides and cholesteryl ester, was decreased in methanolic homogenates. In contrast, due to superior dispersion of precipitates, bead-based homogenization resulted in efficient lipid recovery independent of the solvent composition. However, lipid distribution within samples, i.e., lipid content of supernatant and pellet following centrifugation, was altered substantially by solvent composition. In conclusion, accurate lipid quantification of tissue homogenates requires evaluation of solvent composition, sample concentration, as well as the homogenization method to guarantee efficient lipid recovery. Due to a potential loss of lipids, removal of precipitates by centrifugation prior to lipid extraction should be avoided.

Efficient isolation of brain capillary from a single frozen mouse brain for protein expression analysis

Isolated brain capillaries are essential for analyzing the changes of protein expressions at the blood-brain barrier (BBB) under pathological conditions. The standard brain capillary isolation methods require the use of at least five mouse brains in order to obtain a sufficient amount and purity of brain capillaries. The purpose of this study was to establish a brain capillary isolation method from a single mouse brain for protein expression analysis. We successfully isolated brain capillaries from a single frozen mouse brain by using a bead homogenizer in the brain homogenization step and combination of cell strainers and glass beads in the purification step. Western blot and proteomic analysis showed that proteins expressed at the BBB in mouse brain capillaries isolated by the developed method were more enriched than those isolated from a pool of five mouse brains by the standard method. By using the developed method, we further verified the changes in expression of BBB proteins in Glut1-deficient mouse. The developed method is useful for the analysis of various mice models with low numbers and enables us to understand, in more detail, the physiology and pathology of BBB.

The effect of Gestational Diabetes Mellitus on the fetal compartment

In indicated preterm births such a Gestational Diabetes Mellitus (GDM), little is known about the role of the amnion membranes. Investigating the role of amnion membrane inflammation in response GDM may suggest novel pathophysiologic mechanisms. We hypothesize that increased GDM inflammatory mediators may weaken the amnion membrane predisposing them to infection. Maternal and fetal serum and amnion membrane biopsies were collected from 20 GDM and 38 normoglycemic subjects (control) who underwent elective cesarean sections. Cytokines and adipokines were evaluated in serum and amnion culture supernatant samples. Amnion membrane biopsies from GDM and control subjects were studied: fresh frozen for RNA analysis for Toll-like receptor expression; cultured with LPS to test membrane permeability, and inflammation LPS + anti-TLR4 for testing mechanism. GDM was associated with higher fetal serum leptin (p = 0.004) and IL-10 (p = 0.04) compared to controls. Amnion membrane explants from GDM had higher levels of IL-6 (p = 0.019), and lower expression of Claudin-4 (p = 0.007) and increased permeability (p = 0.046) compared to controls. GDM membranes treated with LPS showed an increased expression of IL-10 (p = 0.013); IL-6 (p = 0.004) and TNF-α (p = 0.0005) but did not affect membrane permeability. LPS and anti-TLR4 antibody treatment reduced the production of TNF-α in controls (p = 0.03) and GDM (p = 0.007) compared to LPS alone. Fetal inflammatory response seems more balanced in GDM and does not impact membrane permeability function even with an infectious stimulus. Light fetal membrane inflammatory response may explain lack of preterm labor in GDM. Concluding, benign inflammation in the membranes may not be harmful for pregnancy maintenance.

Effects of feather processing methods on quantity of extracted corticosterone in broiler chickens

Corticosterone is known as a biological stress index in many species including birds. Feather corticosterone concentration (FCC) has increasingly been used as a measure for chronic stress status in broiler chickens. As sample preparation is the first step of analytical process, different techniques of feather matrix disruption need to be validated for obtaining better result in analysing corticosterone extraction. The current study was a validation of pulverizing the feather by bead beater (BB) and surgical scissors (SS) processing prior to corticosterone extraction in feather of broiler chickens. The type of feather processing prior to the hormone extraction may alter the final output. Thereby, finding a standard method according to laboratory facilities is pivotal. This study carried out to determine the effects of feather pulverization methods on the extraction amount of corticosterone in broiler chickens. Feathers were sampled from four weeks old Ross 308 broiler chickens (n = 12 birds). All broiler chickens were kept under the same environmental condition and had access to feed and water. Feather samples were assigned to one of the following processing methods 1) using a BB for pulverizing and 2) using a SS for chopping into tiny pieces. Each sample was duplicated into two wells during enzyme immunoassay (EIA) analysis to improve the accuracy of the obtained data. The results showed lower standard errors and constant output of FCC by using the BB method compared with the SS method. Overall comparison of FCC showed a significantly higher (p < 0.001) amount of the FCC in the BB compared with the SS. Overall, using the BB method is recommended over the SS method for feather processing due to the ability to homogenize a large number of samples simultaneously, ease of use and greater extraction of feather corticosterone.

Assessment of carbonic anhydrase 3 as a marker for meat authenticity and performance of LC-MS/MS for pork content

In recent years, food fraud is a global issue that has raised wide public concern. Mass spectrometry techniques have a significant advantage of qualitatively and quantitatively analyzing food authenticity, especially for highly processed meat products. In this work, a simple and specific, rapid resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the determination of pork content in processed meat products according to internal standard (ISTD) method. To improve the efficiency of sample preparation, simplified bead-beating and enzymolysis process were investigated. In contrast with different heat-stable and specific porcine-peptides, EPITVSSDQMAK, GGPLTAAYR, HDPSLLPWTASYDPGSAK from Carbonic anhydrase 3 proved to have an excellent quantitative ability, thus obtaining good linear relationship and satisfactory recovery. This method was successfully applied to different types of meat products, thus demonstrating that complex mixtures of pork content can be accurately quantified.

Accelerated Lysis and Proteolytic Digestion of Biopsy-Level Fresh-Frozen and FFPE Tissue Samples Using Pressure Cycling Technology

Pressure cycling technology (PCT)-assisted tissue lysis and digestion have facilitated reproducible and high-throughput proteomic studies of both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tissue of biopsy scale for biomarker discovery. Here, we present an improved PCT method accelerating the conventional procedures by about two-fold without sacrificing peptide yield, digestion efficiency, peptide, and protein identification. The time required for processing 16 tissue samples from tissues to peptides is reduced from about 6 to about 3 h. We analyzed peptides prepared from FFPE hepatocellular carcinoma (HCC) tissue samples by the accelerated PCT method using multiple MS acquisition methods, including short-gradient SWATH-MS, PulseDIA-MS, and 10-plex TMT-based shotgun MS. The data showed that up to 8541 protein groups could be reliably quantified from the thus prepared peptide samples. We applied the accelerated sample preparation method to 25 pairs (tumorous and matched benign) of HCC samples followed by a single-shot, 15 min gradient SWATH-MS analysis. An average of 18 453 peptides from 2822 proteins were quantified in at least 20% samples in this cohort, while 1817 proteins were quantified in at least 50% samples. The data not only identified the previously known dysregulated proteins such as MCM7, MAPRE1, and SSRP1 but also discovered promising novel protein markers, including DRAP1 and PRMT5. In summary, we present an accelerated PCT protocol that effectively doubles the throughput of PCT-assisted sample preparation of biopsy-level FF and FFPE samples without compromising protein digestion efficiency, peptide yield, and protein identification.