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At least 19 records

Predicting High‐Resolution Spatial and Spectral Features in Mass Spectrometry Imaging with Machine Learning and Multimodal Data Fusion

Recent advancements in molecular Mass Spectrometry Imaging have sparked interest in integrating high spatial resolution methods with molecular mass-spectrometry-based chemical imaging. Fusion-based algorithms have proven effective in generating high spatial-resolution molecular mass spectra. However, a significant challenge stems from the differing physical mechanisms underlying image generation and data upsampling techniques, potentially leading to discrepancies in integrated information channels. Integrating physical constraints into data processing workflows is essential to tackle this issue. In this study, we propose an innovative approach that merges data from Fourier transform ion cyclotron resonance (FTICR), time-of-flight matrix-assisted laser desorption/ionization, and time-of-flight secondary ion mass spectrometry imaging techniques. By leveraging FT-ICR's unparalleled spectral resolution and ToF-SIMS's exceptional spatial resolution, we achieve submicron spatial resolution, enabling the observation of intact molecular species with remarkable spectral precision. Canonical correlation analysis is employed to incorporate physical constraints. Through sophisticated image processing and machine learning techniques, the results of this fusion hold significant promise for advancing our comprehension of complex systems and unveiling concealed molecular intricacies.

canonical correlation analysis↗

Desorption Electrospray Ionization–Mass Spectrometry Imaging Provides Spatiochemical Information on Potential Biocontrol Agents against Phytophthora capsici Infection in Tomato Plants

Biological control agents can offer an eco-friendly and more sustainable alternative to conventional chemical pesticides, providing protection against destructive pathogens, such as Phytophthora capsici, while reducing potential environmental harm associated with synthetic pesticide use in agricultural systems. This work evaluates the biocontrol effectiveness of Bacillus vallismortis, Bacillus amyloliquefaciens, Bacillus thuringiensis, and Bacillus subtilis, against the widespread plant pathogen Phytophthora capsici. Our studies showed that Bacillus thuringiensis and Bacillus subtilis promote plant growth and provide protection against Phytophthora capsici in both in vitro and in vivo greenhouse studies, while Bacillus vallismortis and Bacillus amyloliquefaciens were effective in vitro but not in vivo. Specifically, Bacillus thuringiensis was observed to both hinder the growth of Phytophthora capsici and enhance plant resilience to this pathogen, with B. thuringiensis-treated, pathogen-exposed plants displaying a 94.4% increase in root length and a 74.0% increase in shoot height compared to plants with only oomycete exposure. To probe the molecular interactions between the biocontrol agent and pathogen, a dual culture of Bacillus thuringiensis and Phytophthora capsici was analyzed in situ using a desorption electrospray ionization–mass spectrometry imaging (DESI-MSI) workflow. This approach interrogated the spatially oriented biochemical interactions that may serve as the molecular foundation for the effectiveness of these biological control agents in crop protection, identifying seven unique phenotypic regions within the dual culture. Herein, we demonstrate the benefits of biological control agent application in tomato cultivation and showcase the strengths of desorption electrospray ionization–mass spectrometry imaging when applied to the spatially resolved molecular characterization of agriculturally relevant microorganisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single-colony MALDI mass spectrometry imaging reveals spatial differences in metabolite abundance between natural and cultured Trichodesmium morphotypes

Trichodesmium, a globally significant N 2 -fixing marine cyanobacterium, forms extensive surface blooms in nutrient-poor ocean regions. These blooms consist of a dynamic assemblage of Trichodesmium species that form distinct colony morphotypes and are inhabited by diverse microorganisms. Trichodesmium colony morphotypes vary in ecological niche, nutrient uptake, and organic molecule release, differentially impacting ocean carbon and nitrogen biogeochemical cycles. Here, we assessed the poorly studied spatial abundance of metabolites within and between three morphologically distinct Trichodesmium colonies collected from the Red Sea. We also compared these results with two morphotypes of the cultivable Trichodesmium strain IMS101. Using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) coupled with liquid extraction surface analysis (LESA) tandem mass spectrometry (MS2), we identified and localized a wide range of small metabolites associated with single-colony Trichodesmium morphotypes. Our untargeted MALDI-MSI approach revealed 80 unique features (metabolites) shared between Trichodesmium morphotypes. Discrimination analysis showed spatial variations in 57 shared metabolites, accounting for 62% of the observed variation between morphotypes. The greatest variations in metabolite abundance were observed between the cultured morphotypes compared to the natural colony morphotypes, suggesting substantial differences in metabolite production between the cultivable strain IMS101 and the naturally occurring colony morphotypes that the cultivable strain is meant to represent. This study highlights the variations in metabolite abundance between natural and cultured Trichodesmium morphotypes and provides valuable insights into metabolites common to morphologically distinct Trichodesmium colonies, offering a foundation for future targeted metabolomic investigations.

59 BASIC BIOLOGICAL SCIENCES↗

OzMALDI: A Gas-Phase, In-Source Ozonolysis Reaction for Efficient Double-Bond Assignment in Mass Spectrometry Imaging with Matrix-Assisted Laser Desorption/Ionization

Lipids make up an important class of biomolecules with diverse structures and varied chemical functions. This diversity is a major challenge in chemical analysis and limits our understanding of biological functions and regulation. A major way lipid isomers differ is by double-bond (db) position, and analyzing db-isomers is especially challenging for mass spectrometry imaging (MSI). Ozonolysis can be used to determine the dbposition and has been paired with MSI before. However, previous techniques require increased analysis time to allow for gas-phase reactions within an ion trap or ion mobility cell or additional sample preparation time to allow for offline ozonation. Here, we introduce a new ozonolysis method inside the matrix-assisted laser desorption-ionization (MALDI) source, termed OzMALDI, that simultaneously produces ozonides from all unsaturated lipids. This allows us to determine db-positions without adding additional reaction time while maintaining the high mass resolution provided by Orbitrap MS. This new technique is especially effective at determining multiple db-positions in lipids containing polyunsaturated fatty acids, which is a limitation of many previous techniques. OzMALDI-MSI was applied to the analysis of rat brain and genetically engineered Camelina and soybean seed samples, demonstrating the utility of this method and uncovering novel biological information.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Active Humidity Control Chamber for Desorption Electrospray Ionization-Mass Spectrometry Imaging Applications

Ambient ionization techniques enable mass spectrometry (MS) to expand into broader experimental contexts, although it is increasingly clear that results are influenced by the environmental conditions at the site of sampling. Desorption electrospray ionization (DESI), in particular, is affected by variations in relative humidity (RH) levels. Here we describe the design, development, and construction of an environmental control chassis that can actively modulate RH within ± 3% of user-defined set points across a broad humidity range (15%–70% RH). Preliminary characterization demonstrated differential analyte responses across a range of set points, with observed enhancement of leucine-enkephalin, sulfadimethoxine (negative mode), and maltose (positive mode) in response to increased humidity. The measurable differences in analyte signals across discrete humidity set points underscore the importance of environmental control in ambient ionization strategies. The humidity control system outlined here can be translated to other DESI platforms, with construction information provided herein.

DESI↗

Advanced multi-modal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution

The placenta is a complex and heterogeneous organ that links the mother and fetus, playing a crucial role in nourishing and protecting the fetus throughout pregnancy. Integrative spatial multi-omics approaches can provide a systems-level understanding of molecular changes underlying the mechanisms leading to the histological variations of the placenta during healthy pregnancy and pregnancy complications. Herein, we advance our metabolome-informed proteome imaging (MIPI) workflow to include lipidomic imaging, while also expanding the molecular coverage of metabolomic imaging by incorporating on-tissue chemical derivatization (OTCD). The improved MIPI workflow advances biomedical investigations by leveraging state-of-the-art molecular imaging technologies. Lipidome imaging identifies molecular differences between two morphologically distinct compartments of a placental villous functional unit, syncytiotrophoblast (STB) and villous core. Next, our advanced metabolome imaging maps villous functional units with enriched metabolomic activities related to steroid and lipid metabolism, outlining distinct molecular distributions across morphologically different villous compartments. Complementary proteome imaging on these villous functional units reveals a plethora of fatty acid- and steroid-related enzymes uniquely distributed in STB and villous core compartments. Integration across our advanced MIPI imaging modalities enables the reconstruction of active biological pathways of molecular synthesis and maternal-fetal signaling across morphologically distinct placental villous compartments with micrometer-scale resolution.

60 APPLIED LIFE SCIENCES↗

Unimodal Imaging of Monovalent Metal-Chelator Complexes and Lipids by MALDI Imaging Mass Spectrometry

Careful regulation of monovalent metal ions (M + ) is necessary to maintain a functional cellular system. Of these ions, appropriate sodium (Na + ) and potassium (K + ) concentrations are particularly integral for electrochemical signaling, as well as the secondary transport of nutrients and waste. Dysregulation of M + homeostasis can disrupt these mechanisms, potentially influencing the metabolism of downstream biomolecules such as lipids. Thus, the relationship between M + abundances and related biomolecular distributions must be elucidated to better understand the physiology of healthy and disordered tissues. Traditional techniques for imaging biological metal distributions include SIMS, LA-ICP-MS, and XRF; however, these capabilities are limited to elemental analysis or the analysis of molecular fragments and must be paired with other modalities to visualize distributions of more complex biomolecules within the same or similar samples. Conversely, matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful tool often used for mapping such biomolecular distributions, but current methods are unable to detect metals within tissue. This study illustrates a novel methodology that adds metal detection to the MALDI IMS repertoire through which the simultaneous detection of M + metals and lipids is achievable. Using a robotic sprayer for homogeneous application, on-tissue deposition of the chelator deferiprone (DEF) enables subsequent detection of the ionizable metal-chelator complex by MALDI without hindering lipid detection. Our work provides proof-of-concept data for the simultaneous detection of K + , Na + , and intact lipids using MALDI IMS.

59 BASIC BIOLOGICAL SCIENCES↗

Spatial top-down proteomics for the functional characterization of human kidney

Background: The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. Results: Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. Conclusions: We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.

59 BASIC BIOLOGICAL SCIENCES↗

Spatial Glycomics and Kidney Disease

Glycans are critical for the kidney's physiological and pathological cellular functions, and our ability to reveal their spatial distributions within tissues has helped us reveal how these carbohydrate moieties are involved in many of these processes. This review discusses the role of different types of glycans in kidney biology and disease, common approaches used for glycan imaging, and how glycan imaging has helped us better understand kidney pathology. Here, we mainly focus on emerging methods using mass spectrometry imaging (MSI) because this technology is untargeted and provides complete information on glycan composition compared to the other methods, such as lectin and metabolite labeling, which are targeted and often inform only on the specific part of a glycan structure. We especially focus on protein N-glycosylation, as this is one of the most common post-translational modifications, and these moieties play a vital role in renal structure and function. The recent advancements in MSI of N-glycans we reviewed have provided new insights into the pathophysiology of the kidney and paved the way for clinical application.

60 APPLIED LIFE SCIENCES↗

Spatial metabolomics and lipidomics in kidney disease

Kidney disease is a global health issue that affects over 850 million people, and early detection is key to preventing severe disease and complications. Kidney diseases are associated with complex dysregulation of lipid metabolism. Spatial metabolomics through mass spectrometry imaging (MSI) enables spatial mapping of the lipids in tissue and includes a variety of techniques that can be used to image lipids. In the kidney MSI studies often seek to resolve individual functional tissue units such as glomeruli and proximal tubules. Several different MSI techniques such as matrix-assisted laser desorption/ionization and desorption electrospray ionization have been used to characterize lipids and small molecules in chronic kidney disease, acute kidney injury, genetic kidney disease, and cancer. In this review we provide several examples of how spatial metabolomics data can provide critical information concerning localization of changes in disease states. Additionally, when combined with pathology, measurements, transcriptomics, or proteomics, the metabolomic changes can illuminate underlying mechanisms and provide new clinical insights.

59 BASIC BIOLOGICAL SCIENCES↗

A Fast-Pass, Desorption Electrospray Ionization Mass Spectrometry Strategy for Untargeted Metabolic Phenotyping

Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) provides direct analytical readouts of small molecules that can be used to characterize the metabolic phenotypes of genetically engineered bacteria. In an effort to accelerate the time frame associated with the screening of mutant libraries, we have developed a high-throughput DESI-MSI analytical workflow implementing a single raster line-scan strategy that facilitates the collection of location-resolved molecular information from engineered strains on a subminute time scale. Evaluation of this “Fast-Pass” DESI-MSI phenotyping workflow on analytical standards demonstrated the capability of acquiring full metabolic profiling information with a throughput of ~40 s per sample. This Fast-Pass strategy was implemented in the analysis of genetically edited Escherichia coli strains that have been engineered to produce various free-fatty acids (FFAs) for applications relevant to biofuels. Due to the untargeted nature of DESI-MSI, the investigation of these strains yielded molecular information for both global metabolites and targeted detection of accumulated bioproducts, allowing simultaneous readouts of strain-specific chemical profiles and comparative measurements of FFA production levels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Integrating N -glycan and CODEX imaging reveal cell-specific protein glycosylation in healthy human lung

Identifying cell-specific glycan structures in human lungs is critical for understanding the chemistry and mechanisms that guide cell–cell and cell–matrix interactions and determining nuanced functions of specific glycosylation. Our dual-modality omics platform, which uses matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to profile glycan chemistry at 50 μm × 50 μm scale, combined with co-detection by indexing (CODEX) to provide cell identification from the exact same tissue section, is a significant step in this direction. It enabled us to detect, differentiate, and reveal chemical properties of N-glycans in the various cell types of a human lung, suggesting the cell-specific function of distinct carbohydrate moieties. This innovative technological combination bridges the gap between the specific protein glycosylation and their cellular origin, paving the way for targeted studies in the lungs and many other human tissues where glycans mediate cell–cell recognition events.

Veličković, Dušan [Pacific Northwest National Labo↗

Untargeted Spatial Metabolomics and Spatial Proteomics on the Same Tissue Section

An increasing number of spatial multiomic workflows have been recently developed. Some of these approaches have leveraged initial mass spectrometry imaging (MSI)-based spatial metabolomics to inform region of interest (ROI) selection for downstream spatial proteomics. However, these workflows have been limited by varied substrate requirements between modalities or have required analyzing serial sections (i.e., one section per modality). To mitigate these issues, we present a novel multiomic workflow that uses desorption electrospray ionization (DESI)-MSI to identify representative spatial metabolite patterns on-tissue prior to spatial proteomic analyses on the same tissue section. Further, this workflow is demonstrated here with a model mammalian tissue (coronal rat brain section) mounted on a polyethylene naphthalate-membrane slide. Initial DESI-MSI resulted in 160 annotations (SwissLipids) within to the METASPACE platform (≤20% false discovery rate). A segmentation map from the annotated ion images informed downstream ROI selection for spatial proteomics characterization from the same sample. The unspecific substrate requirements and minimal sample disruption inherent to DESI-MSI allowed for an optimized, downstream spatial proteomics assay, resulting in 3888 ± 240 to 4717 ± 48 proteins being confidently directed per ROI (200 µm x 200 µm). Finally, we demonstrate the integration of multiomic information, where we found ceramide localization to be correlated with SMPD3 abundance (ceramide synthesis protein), and we also utilized protein abundance to resolve metabolite isomeric ambiguity. Overall, the integration of DESI-MSI into the multiomic workflow allows for complementary spatial and molecular-level information to be achieved from optimized implementations of each MS assay inherent to the workflow itself.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental and Computational Evaluation of Lipidomic In-Source Fragmentation as a Result of Postionization with Matrix-Assisted Laser Desorption/Ionization

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can provide spatially resolved molecular information about a sample. Recently, a postionization approach (MALDI-2) has been commercially integrated with MALDI-MSI, allowing for bettered sensitivity and consequent improved spatial resolution. While advantages of MALDI-2 have previously been established, we demonstrate here statistically increased in-source fragmentation (ISF) results from postionization with a commercial instrument. Via lipid standard analyses, known MALDI ISF pathways (e.g., loss of trimethylamine) were statistically increased in MALDI-2 compared to MALDI-1 (65–172% increase in fragmentation). Gas phase molecular modeling with density functional theory estimated that the most-weighted virtual orbitals to excite within lipids involve ester and phosphate bonds. Protonated lipid excitation energies are furthermore red-shifted compared to those of other adduct types [e.g., 254 nm for protonated PC(16:0/18:1)] and approach the MALDI-2 laser energy (266 nm). Analysis of rat brain homogenate detected statistically more positive-ion mode peaks with MALDI-2 (1090) than that with MALDI-1 (719), where Kernel density estimations showed that the majority of this enhancement occurs with low m/z ions (i.e., m/z 75–500). Taken together with the lipid standard data, these observations may indicate ISF due to postionization. Finally, while artifact contributions from matrix blanks were also noted, both experimental and computational data sets suggest that the overall extent of ISF is statistically increased in MALDI-2 compared to MALDI-1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Step-by-Step Protocol from METASPACE to Biological Interpretation

Mass spectrometry imaging (MSI) represents an exceptional tool for exploring complex biological systems spatially at the molecular level. However, due to its multidimensional nature and large-scale data output, it presents considerable challenges when it comes to extracting meaningful biological insights. Recent advancements, such as the METASPACE platform, have enabled researchers to efficiently process, annotate, and interpret MSI datasets by leveraging machine learning and cloud-based infrastructure. In this tutorial, we present a detailed and user-friendly R-pipeline designed to help METASPACE users navigate untargeted metabolomic annotations and transform them into practical insights about their biological systems. By combining METASPACE annotations with rapid R-based screening, this workflow not only streamlined the analytical process but also enhanced the understanding of spatial molecular distribution, especially for complex systems. Here, this easy-to-follow approach has the potential for applications in diagnostics, drug discovery, environmental and ecological processes, and more. We envision this pipeline to be particularly useful for newcomers to the field of MSI and

Moreno Pedraza, Abigail↗

Characterization of the biofilm landscape of Bacillus subtilis by spatial microproteomics

Bulk proteomics has been demonstrated to differentiate subpopulations within bacterial colonies, yet advanced analyses by mass spectrometry imaging (MSI) hold even greater promise for the future. This technology can enable high-throughput spatial phenotyping that can reshape biological discovery by providing visualization of components of various biomolecular mechanisms. With high mass resolving power and high spatial resolution analyses being routine, we can confidently enable intact protein imaging directly from samples with minimal preparation. Pairing those analyses with bulk experimental libraries can provide high confidence in annotations of post-translational modifications (PTMs) and truncations. Revealing PTM localization within the samples unlocks a direct window into unknown biology at the microscale. However, top-down proteomics (TDP) is not commonplace for microbial species, largely due to challenges in identifying detected peptides and proteins; considering the theoretical proteome of even the well-studied model bacterium Bacillus subtilis was only partially mapped recently. With little still known about the form and function of many of these proteins – let alone proteoforms, where PTMs and truncations of the same protein may possess unique physiological roles – there is a wealth of work to be done. Here we jointly apply TDP and MSI to describe the microscale spatial proteomic landscape within B. subtilis and further demonstrate the feasibility of detecting differentiated subpopulations through proteoforms across the biofilm landscape.

bacterial biofilms↗

Getting to the root of the problem: Soil carbon and microbial responses to root inputs within a buried paleosol along an eroding hillslope in southwestern Nebraska, USA

Large quantities of soil carbon (C) can persist within paleosols for millennia due to burial and subsequent isolation from plant-derived inputs, atmospheric conditions, and microbial activity at the modern surface. Erosion exposes buried soils to modern root-derived C influx via root exudation and root turnover, thus stimulating microbial activity leading to SOC decomposition and accumulation through organo-mineral stabilization of modern C. With this study we aim to quantify how modern root-derived C inputs impact paleosol C decomposition and stabilization across varying degrees of isolation from modern surface conditions in southwestern Nebraska, USA, where hillslope erosion is bringing a buried Late-Pleistocene-early Holocene paleosol (the “Brady Soil”) closer to the modern surface. We collected Brady Soil samples from 0.2m, 0.4m, and 1.2m below the modern surface and conducted two lab-based incubations. Soils were amended with either (1) a lab-synthesized mixture of low molecular weight compounds (12 atom% 13 C), or (2) 13 C enriched root residues (92 atom% 13 C), in 30-day and 240-day incubation experiments, respectively. Here we determined microbial responses to synthetic root exudates and residues by partitioning the 13 C label from Brady Soil C, including measurements of total, root, and primed C respiration, microbial biomass C (MBC), microbial C use efficiency (CUE). To assess the capacity of isolated paleosols to accrue modern plant C, we used Nano-scale Secondary Ion Mass Spectrometry imaging. We found that: (1) adding root-derived C inputs primed Brady Soil C across all depths, and was mediated by depth and composition of root additions; (2) root-derived C inputs stimulated microbial biomass C (MBC) growth similarly across depths, but the magnitude of CUE and MBC varied by chemistry of root-derived additions; (3) new particulate organic matter was incorporated into mineral-associated pools over time; (4) material from the added root residues was found in association with bacterial cells and fungal hyphae as well as with soil aggregate and mineral surfaces. Our study shows that paleosols defy expectations of C content and reactivity with depth, and changes in land cover and climate will expose buried paleosols to modern surface conditions, increasing respired C. This work highlights the importance of evaluating the role resurfacing buried soils through landscape change plays in C cycle feedbacks to the climate system.

54 ENVIRONMENTAL SCIENCES↗

Protein N -Glycans in Healthy and Sclerotic Glomeruli in Diabetic Kidney Disease

Diabetes is expected to directly affect renal glycosylation; yet to date, there has not been a comprehensive evaluation of alterations in N-glycan composition in the glomeruli of patients with diabetic kidney disease (DKD). Here, we used untargeted mass spectrometry imaging to identify N-glycan structures in healthy and sclerotic glomeruli in formalin-fixed paraffin-embedded sections from needle biopsies of five patients with DKD and three healthy kidney samples. Regional proteomics was performed on glomeruli from additional biopsies from the same patients to compare the abundances of enzymes involved in glycosylation. Secondary analysis of single-nucleus RNA sequencing (snRNAseq) data were used to inform on transcript levels of glycosylation machinery in different cell types and states. We detected 120 N-glycans, and among them, we identified 12 of these protein post-translated modifications that were significantly increased in glomeruli. All glomeruli-specific N-glycans contained an N-acetyllactosamine epitope. Five N-glycan structures were highly discriminant between sclerotic and healthy glomeruli. Sclerotic glomeruli had an additional set of glycans lacking fucose linked to their core, and they did not show tetra-antennary structures that were common in healthy glomeruli. Orthogonal omics analyses revealed lower protein abundance and lower gene expression involved in synthesizing fucosylated and branched N-glycans in sclerotic podocytes. In snRNAseq and regional proteomics analyses, we observed that genes and/or proteins involved in sialylation and N-acetyllactosamine synthesis were also downregulated in DKD glomeruli, but this alteration remained undetectable by our spatial N-glycomics assay. Integrative spatial glycomics, proteomics, and transcriptomics revealed protein N-glycosylation characteristic of sclerotic glomeruli in DKD.

60 APPLIED LIFE SCIENCES↗