Biology subjects

Heeren, R. M. A.

Publications and source records attributed to Heeren, R. M. A..

9 recordsLinked to original sources

bioRxiv2026

Spatial Single Cell Lipid-Transcriptomic Coupling Reveals Metabolic Niches in Glioblastoma

Glioblastoma is characterized by spatial heterogeneity, with tumor-core and invasive-edge regions differing in cellular composition, transcriptional state, and metabolic context. Spatial transcriptomics has improved understanding of glioblastoma tissue organization. However, cellular transcriptional programs and metabolic interpretation remain poorly resolved. Here, single-cell matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) with spatial transcriptomics were integrated on the same tissue sections to map lipid and transcriptomic organization across matched tumor-core and invasive-region samples from 10 glioblastoma patients. Common region-dependent cellular organization along the core - versus invasive regions were identified after accounting for patient specific signatures. Tumor cores were enriched with astrocyte-like malignant and immune cell types, whereas invasive regions showed increased contribution from oligodendrocyte (progenitor cells). Despite these compositional differences, tumor and invasive cells had a shared transcriptional state space, indicating that regional identity is shaped by altered spatial organization of shared cell states. Transcriptional programs associated with proliferation, hypoxia, extracellular matrix remodeling, tumor associated macrophages and microglia (TAMs) phagocytic activity, T-cell infiltration, and lipid synthesis were spatially structured and differed between tumor and invasive compartments. MALDI-MSI revealed broad lipidomic remodeling across these regions. Tumor regions were enriched in membrane and storage lipid classes, whereas invasive regions showed relative enrichment of lipid species associated with membrane turnover. Integrating lipid and transcriptomic layers revealed spatial lipid-gene program coupling, with tumor cores showing stronger and more coherent coupling than invasive regions. TAM phagocytic activity co-localized with cholesteryl ester abundance, while lipid synthesis coupled to phosphatidylcholine-rich astrocyte-like tumor niches. Exploratory analysis indicated that MGMT promoter methylation may be associated with this altered lipid-transcriptional coupling, particularly in TAM-associated lipid-handling programs. Together, these findings imply that spatial coordination between lipid states and transcriptional programs is a key feature of glioblastoma metabolic heterogeneity.

molecular biology↗

bioRxiv2026

Thyra: Bridging Mass Spectrometry Imaging and SpatialData for Unified Multi-Modal Analysis

Mass Spectrometry Imaging (MSI) is a powerful technique for mapping molecular distributions, and its integration with other imaging modalities is crucial for comprehensive understanding of molecular systems. Fragmented data formats and the limitations of existing standards like imzML, challenge spatial biology centric multi-modal data analysis and adherence to FAIR data principles. This paper introduces Thyra, a modern Python library designed to convert MSI data into the SpatialData framework, a unified and extensible multi-platform file format that crucially integrates MSI into the broader spatial omics ecosystem. Thyras modular architecture, intelligent mass axis resampling, and sparse matrix backend address performance bottlenecks and facilitate seamless integration with tools for advanced spatial statistics and visualization. By adopting SpatialData, Thyra not only improves data interoperability, accessibility, and reusability, but also unlocks new avenues for multi-modal research, empowering scientists to integrate rich chemical information into diverse biological workflows.

bioinformatics↗

bioRxiv2025

One Section, Two Worlds: Single-Cell Integration of MALDI-MSI and Spatial Transcriptomics on the Same Single Tissue Section

Understanding tissue complexity requires spatially resolved multiomic data at single-cell resolution. Here, we present a workflow that integrates high-resolution matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) with Xenium spatial transcriptomics (SPT) on a single tissue section. This one-section strategy ensures exact spatial correspondence between metabolic and transcriptomic features, avoiding the misalignment issues of serial sections, where even minor offsets can result in sampling different cells. We validate compatibility of MALDI-MSI with downstream SPT, preserving transcriptomic quality despite semi-destructive ionization. Using mouse brain and human glioblastoma tissues, we achieve pixel-perfect modality coregistration, enabling per-cell MALDI spectra extraction aligned with gene expression. Integrated clustering reveals enhanced cell-type resolution and identifies metabolic heterogeneity within transcriptionally defined populations. This enables a direct and precise correlation between what a cell is doing and its biochemical state, providing a more holistic and accurate picture of cellular function, heterogeneity, and interaction in health and disease. Our workflow provides a scalable path to multiomic atlases of disease and development, advancing both data integration and translational research.

molecular biology↗

bioRxiv2025

Ontogeny-independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis

Granulomas are organized inflammatory lesions that form in response to persistent stimuli such as infections. Murine infection with Leishmania donovani results in the formation of granulomas around infected Kupffer cells in the liver and serves as a well-defined model of immune granuloma formation. The formation and resolution of granulomatous inflammation requires dynamic shifts in immune cell activation states, imposing significant metabolic demands. As mediators of energy homeostasis and cell signaling, lipids and lipid metabolism play a key role in regulating immune cell function during inflammation and the response to infection. However, the extent to which alterations in lipids are spatially linked to altered immune cell transcription has yet to be resolved. In this study, we performed a multimodal imaging analysis combining MALDI mass spectrometry, spatial and single cell transcriptomics, proteomics of flow-sorted macrophages and histopathology of L. donovani induced hepatic granulomas. Using this spatially-integrated approach, we identified LPCAT2-mediated membrane re-modelling of myeloid cells as a novel feature of these granulomas. Our study provides new insights into local immunometabolic changes associated with granuloma formation and macrophage activation.

immunology↗

bioRxiv2024

High-resolution metabolite imaging: luteolinidin accumulates at the host-cyanobiont interface during cold-acclimation in Azolla symbioses

Aquatic ferns of the genus Azolla (Azolla) form highly productive symbioses with filamentous cyanobacteria fixing N2 in their leaf cavities, Nostoc azollae. Stressed symbioses characteristically turn red due to 3-deoxyanthocyanin (DA) accumulation, rare in angiosperms and of unknown function. To reveal DA functions upon cold acclimation and recovery, we integrated laser-desorption-ionization mass-spectrometry-imaging (LDI-MSI), a new A. filiculoides genome-assembly and annotation, and dual RNA-sequencing into phenotypic analyses of the symbioses. Azolla sp. Anzali recovered even when cold-induced DA-accumulation was inhibited by abscisic acid. Cyanobacterial filaments generally disappeared upon cold acclimation, and N. azollae transcript profiles were unlike those of resting stages formed in cold-resistant sporocarps, yet filaments re-appeared in leaf cavities of newly formed green fronds upon cold-recovery. The high transcript accumulation upon cold acclimation of AfDFR1 encoding a flavanone 4-reductase active in vitro suggested that the enzyme of the first step in the DA-pathway may regulate accumulation of DAs in different tissues. However, LDI-MSI highlighted the necessity to describe metabolite accumulation beyond class assignments as individual DA and caffeoylquinic acid metabolites accumulated differentially. For example, luteolinidin accumulated in epithelial cells, including those lining the leaf cavity, supporting a role for the former in the symbiotic interaction during cold acclimation. Summary statementDuring cold acclimation in Azolla symbioses, individual compounds from the same phenolic class accumulated in different host tissues: luteolinidin associated with biotic interactions at the symbiosis interface whilst apigenidin with photooxidative stress mitigation in the mesophyll.

plant biology↗

bioRxiv2023

Omics Scale Quantitative Mass Spectrometry Imaging of Lipids in Brain Tissue using a Multi-Class Internal Standard Mixture

Mass spectrometry imaging (MSI) has accelerated the understanding of lipid metabolism and spatial distribution in tissues and cells. However, few MSI studies have approached lipid imaging quantitatively and those that have focus on a single lipid class. Herein, we overcome limitation of quantitative MSI (Q-MSI) by using a multi-class internal standard lipid mixture that is sprayed homogenously over the tissue surface with analytical concentrations that reflects endogenous brain lipid levels. Using this approach we have performed Q-MSI for 13 lipid classes representing >200 sum-composition lipid species. This was carried out using both MALDI (negative ion mode) and MALDI-2 (positive ion mode) and pixel-wise normalisation of each lipid species signal to the corresponding class-specific IS an approach analogous to that widely used for shotgun lipidomics from biological extracts. This approach allows pixel concentrations of lipids to be reported in pmol/mm2. Q-MSI of lipids covered 3 orders of magnitude in dynamic range and revealed subtle change sin in distribution compared to conventional total-ion-current normalisation approaches. The robustness of the method was evaluated by repeating experiments in two laboratories on biological replicates using both timsTOF and Orbitrap mass spectrometers operated with a ~4-fold difference in mass resolution power. There was a strong overall correlation in the Q-MSI result obtained using the two approaches with outliers mostly rationalised by isobaric interferences that are only resolved with the Orbitrap system or the higher sensitivity of one instrument for particular lipid species, particularly for lipids detected at low intensity. These data provide insight into how mass resolving power can affect Q-MSI data. This approach opens up the possibility of performing large-scale Q-MSI studies across numerous lipid classes and reveal how absolute lipid concentrations vary throughout and between biological tissues.

biochemistry↗

bioRxiv2021

Isomeric lipid signatures reveal compartmentalised fatty acid metabolism in cancer

1.0Cellular energy and biomass demands of cancer drive a complex dynamic between uptake of extracellular fatty acids (FA) and de novo synthesis. Given that oxidation of de novo synthesised FAs for energy would result in net-energy loss, there is an implication that FAs from these two sources must have distinct metabolic fates - however hitherto FAs were considered part of a common pool. To probe FA metabolic partitioning, cancer cells were supplemented with stable-isotope labelled FAs. Structural analysis of the resulting glycerophospholipids revealed that labelled FAs from uptake were largely incorporated to canonical (sn-)positions on the glycerol backbone. Surprisingly, labelled FA uptake disrupted canonical isomer patterns of the unlabelled lipidome and induced repartitioning of n-3 and n-6 polyunsaturated-FAs into glycerophospholipid classes. These structural changes evidence differences in the metabolic fate of FAs derived from uptake or de novo sources and demonstrate unique signalling and remodelling behaviours usually hidden to conventional lipidomics. HighlightsO_LILipid isomers reveal discrete metabolic compartmentalisation in cancer C_LIO_LIFAs derived from uptake and de novo synthesis have different metabolic fates C_LIO_LIStearate uptake signals for PUFA (n-3 and n-6) repartitioning between lipid classes C_LIO_LIsn-positional isomers are a marker for aberrant lipid metabolism C_LI

cancer biology↗

bioRxiv2021

Sphingolipid Control of Fibroblast Heterogeneity Revealed by Single-Cell Lipidomics

Human cells produce thousands of lipids that impact a wide range of biological processes in ways we are only starting to characterize. The cellular composition in lipids changes during differentiation events and also varies across individual cells of the same type. Yet, the precise differences in lipid composition that directly affect cell phenotypes remain unknown. Here we have measured the lipidomes and transcriptomes of individual human dermal fibroblasts by coupling high-resolution mass spectrometry imaging to single-cell transcriptomics. We found that the cell-to-cell variation of specific lipid metabolic pathways contributes to the establishment of cell states involved in wound repair and in skin cancer growth. Sphingolipid composition defined fibroblast subpopulations while sphingolipid metabolic rewiring drove cell state transitions. These data uncover a role for cell-to-cell lipid heterogeneity in the determination of cell states and reveal a new regulatory component to the homeostasis and self-organization of multicellular systems.

biochemistry↗

bioRxiv2020

Mass spectrometry imaging of phosphatidylcholine metabolism in lungs administered with therapeutic surfactants and isotopic tracers

Mass spectrometry imaging (MSI) visualises molecular distributions throughout tissues but is blind to dynamic metabolic processes. Here, MSI with high mass resolution together with multiple stable isotope labelling provided spatial analyses of phosphatidylcholine (PC) metabolism in mouse lungs. Dysregulated surfactant metabolism is central to many respiratory diseases. Metabolism and turnover of therapeutic pulmonary surfactants were imaged from distributions of intact and metabolic products of an added tracer, universally 13C-labelled dipalmitoyl PC (U[13C]DPPC). The parenchymal distributions of newly synthesised PC species were also imaged from incorporations of methyl-D9-choline. This dual labelling strategy demonstrated both lack of inhibition of endogenous PC synthesis by exogenous surfactant and location of acyl chain remodelling processes acting on the U[13C]DPPC-labelled surfactant, leading to formation of polyunsaturated PC lipids. This ability to visualise discrete metabolic events will greatly enhance our understanding of lipid metabolism in diverse tissues, and has potential application to both clinical and experimental studies.

biochemistry↗