Tissue Sampling and Homogenization in the Sub-Microliter Scale with a Nanosecond Infrared Laser (NIRL) for Mass Spectrometric Proteomics

Clinical glycoproteomics: methods and diseases

Glycoproteins, representing a significant proportion of posttranslational products, play pivotal roles in various biological processes, such as signal transduction and immune response. Abnormal glycosylation may lead to structural and functional changes of glycoprotein, which is closely related to the occurrence and development of various diseases. Consequently, exploring protein glycosylation can shed light on the mechanisms behind disease manifestation and pave the way for innovative diagnostic and therapeutic strategies. Nonetheless, the study of clinical glycoproteomics is fraught with challenges due to the low abundance and intricate structures of glycosylation. Recent advancements in mass spectrometry-based clinical glycoproteomics have improved our ability to identify abnormal glycoproteins in clinical samples. In this review, we aim to provide a comprehensive overview of the foundational principles and recent advancements in clinical glycoproteomic methodologies and applications. Furthermore, we discussed the typical characteristics, underlying functions, and mechanisms of glycoproteins in various diseases, such as brain diseases, cardiovascular diseases, cancers, kidney diseases, and metabolic diseases. Additionally, we highlighted potential avenues for future development in clinical glycoproteomics. These insights provided in this review will enhance the comprehension of clinical glycoproteomic methods and diseases and promote the elucidation of pathogenesis and the discovery of novel diagnostic biomarkers and therapeutic targets.

Optimization of lung tissue pre-treatment by bead homogenization for subsequent culturomics

The discovery that the lung harbors a diverse microbiome, as revealed by next-generation sequencing, has significantly altered our understanding of respiratory health and disease. Despite the association between the lung microbiota and disease, the nature of their relationship remains poorly understood, and culture isolation of these microorganisms could help to determine their role in lung physiology. Current procedures for processing samples from the lower respiratory tract have been shown to affect the viability of microorganisms, so it is crucial to develop new methods to improve their survival. This study aimed to improve the isolation and characterization of lung microorganisms using a bead-beating homogenization method in a mouse model. Microsphere diameter and bead-beating time affected the survival of the microorganisms (E. coli, S. aureus and C. albicans). Using 2.3 mm diameter microspheres for 60 s of bead-beating promoted the survival of both bacteria and yeast strains. After intratracheal instillation of these microorganisms in mice, approximately 70% of the cells were recovered after the tissue homogenization. To assess the efficiency of the proposed method, the diversity of bacteria was compared between the homogenate and lung tissue samples. Ninety-one genera were detected in the lung tissue, and 63 in the homogenate. Bacterial genera detected in the homogenate represented 84% of the total abundance of the microbiota identified in the lung tissue. Taken together, these results demonstrate that the tissue homogenization process developed in this study recovered the majority of the microorganisms present in the lung. This study presents a bead-beating homogenization method for effective cultivation of lung tissue microorganisms, which may help to improve the understanding of host-microbe interactions in the lung.

Nanosecond infrared laser (NIRL) for cutting roots of human teeth: thermal effects and quality of cutting edges

A nanosecond infrared laser (NIRL) was investigated in cutting dental roots. The focus of the investigation was defining the preparation accuracy and registration of thermal effects during laser application. Ten teeth were processed in the root area using a NIRL in several horizontal, parallel incisions to achieve tooth root ablation as in an apicoectomy. Temperature change was monitored during ablation and the quality of the cutting edges in the roots were studied by means of micro-CT, optical coherence tomography, and histology of decalcified and undecalcified specimens. NIRL produced clearly defined cut surfaces in dental hard tissues. The automated guidance of the laser beam created regular, narrow dentin defects that tapered in a V-shape towards the ablation plane. A biologically significant increase in the temperature of the object and its surroundings did not occur during the laser application. Thermal dentin damage was not detected in histological preparations of treated teeth. Defined areas of the tooth root may be ablated using a NIRL. For clinical translation of NIRL in apicoectomy, it would be necessary to increase energy delivered to hard tissue and develop beam application facilitating beam steering for oral treatment.

Direct 3D Sampling of the Embryonic Mouse Head: Layer-wise Nanosecond Infrared Laser (NIRL) Ablation from Scalp to Cortex for Spatially Resolved Proteomics

Common workflows in bottom-up proteomics require homogenization of tissue samples to gain access to the biomolecules within the cells. The homogenized tissue samples often contain many different cell types, thereby representing an average of the natural proteome composition, and rare cell types are not sufficiently represented. To overcome this problem, small-volume sampling and spatial resolution are needed to maintain a better representation of the sample composition and their proteome signatures. Using nanosecond infrared laser ablation, the region of interest can be targeted in a three-dimensional (3D) fashion, whereby the spatial information is maintained during the simultaneous process of sampling and homogenization. In this study, we ablated 40 μm thick consecutive layers directly from the scalp through the cortex of embryonic mouse heads and analyzed them by subsequent bottom-up proteomics. Extra- and intracranial ablated layers showed distinct proteome profiles comprising expected cell-specific proteins. Additionally, known cortex markers like SOX2, KI67, NESTIN, and MAP2 showed a layer-specific spatial protein abundance distribution. We propose potential new marker proteins for cortex layers, such as MTA1 and NMRAL1. The obtained data confirm that the new 3D tissue sampling and homogenization method is well suited for investigating the spatial proteome signature of tissue samples in a layerwise manner. Characterization of the proteome composition of embryonic skin and bone structures, meninges, and cortex lamination in situ enables a better understanding of molecular mechanisms of development during embryogenesis and disease pathogenesis.

Lipidome Analysis of Oropharyngeal Tumor Tissues Using Nanosecond Infrared Laser (NIRL) Tissue Sampling and Subsequent Mass Spectrometry

Ultrashort pulse infrared lasers can simultaneously sample and homogenize biological tissue using desorption by impulsive vibrational excitation (DIVE). With growing attention on alterations in lipid metabolism in malignant disease, mass spectrometry (MS)-based lipidomic analysis has become an emerging topic in cancer research. In this pilot study, we investigated the feasibility of tissue sampling with a nanosecond infrared laser (NIRL) for the subsequent lipidomic analysis of oropharyngeal tissues, and its potential to discriminate oropharyngeal squamous cell carcinoma (OPSCC) from non-tumorous oropharyngeal tissue. Eleven fresh frozen oropharyngeal tissue samples were ablated. The produced aerosols were collected by a glass fiber filter, and the lipidomes were analyzed with mass spectrometry. Data was evaluated by principal component analysis and Welch's t-tests. Lipid profiles comprised 13 lipid classes and up to 755 lipid species. We found significant inter- and intrapatient alterations in lipid profiles for tumor and non-tumor samples (p-value < 0.05, two-fold difference). Thus, NIRL tissue sampling with consecutive MS lipidomic analysis is a feasible and promising approach for the differentiation of OPSCC and non-tumorous oropharyngeal tissue and may provide new insights into lipid composition alterations in OPSCC.

Proteomic Landscape of Human Spermatozoa: Optimized Extraction Method and Application

Human spermatozoa proteomics exposed to some physical, biological or chemical stressors is being explored. However, there is a lack of optimized sample preparation methods to achieve in-depth protein coverage for sperm cells. Meanwhile, it is not clear whether antibiotics can regulate proteins to affect sperm quality. Here, we systematically compared a total of six different protein extraction methods based the combination of three commonly used lysis buffers and physical lysis strategies. The urea buffer combined with ultrasonication (UA-ultrasonication) produced the highest protein extraction rate, leading to the deepest coverage of human sperm proteome (5685 protein groups) from healthy human sperm samples. Since the antibiotics, amoxicillin and clarithromycin, have been widely used against H. pylori infection, we conduct a longitudinal study of sperm proteome via data-independent acquisition tandem mass spectrometry (DIA-MS/MS) on an infected patient during on and off therapy with these two drugs. The semen examination and morphological analysis were performed combined with proteomics analysis. Our results indicated that antibiotics may cause an increase in the sperm concentration and the rate of malformed sperm and disrupt proteome expression in sperm. This work provides an optimized extraction method to characterize the in-depth human sperm proteome and to extend its clinical applications.

Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine

For investigating the molecular physiology and pathophysiology in organs, the most exact data should be obtained; if not, organ-specific cell lines are analyzed, or the whole organ is homogenized, followed by the analysis of its biomolecules. However, if the morphological organization of the organ can be addressed, then, in the best case, the composition of molecules in single cells of the target organ can be analyzed. Laser capture microdissection (LCM) is a technique which enables the selection of specific cells of a tissue for further analysis of their molecules. However, LCM is a time-consuming two-dimensional technique, and optimal results are only obtained if the tissue is fixed, e.g., by formalin. Especially for proteome analysis, formalin fixation reduced the number of identifiable proteins, and this is an additional drawback. Recently, it was demonstrated that sampling of fresh-frozen (non-fixed) tissue with an infrared-laser is giving higher yields with respect to the absolute protein amount and number of identifiable proteins than conventional mechanical homogenization of tissues. In this study, the applicability of the infrared laser tissue sampling for the proteome analysis of different cell layers of murine intestine was investigated, using LC–MS/MS-based differential quantitative bottom-up proteomics. By laser ablation, eight consecutive layers of colon tissue were obtained and analyzed. However, a clear distinguishability of protein profiles between ascending, descending, and transversal colon was made, and we identified the different intestinal-cell-layer proteins, which are cell-specific, as confirmed by data from the Human Protein Atlas. Thus, for the first time, sampling directly from intact fresh-frozen tissue with three-dimensional resolution is giving access to the different proteomes of different cell layers of colon tissue.

Infrared Laser Ablation Microsampling with a Reflective Objective

A Schwarzschild reflective objective with a numerical aperture of 0.3 and working distance of 10 cm was used for laser ablation sampling of tissue for off-line mass spectrometry. The objective focused the laser to a diameter of 5 μm and produced 10 μm ablation spots on thin ink films and tissue sections. Rat brain tissue sections 50 μm thick were ablated in transmission geometry, and the ablated material was captured in a microcentrifuge tube containing solvent. Proteins from ablated tissue sections were quantified with a Bradford assay, which indicated that approximately 300 ng of protein was captured from a 1 mm² area of ablated tissue. Areas of tissue ranging from 0.01 to 1 mm² were ablated and captured for bottom-up proteomics. Proteins were extracted from the captured tissue and digested for liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis for peptide and protein identification.