Biology subjects

Colley, M. E.

Publications and source records attributed to Colley, M. E..

7 recordsLinked to original sources

bioRxiv2026

Multimodal Imaging of the Cellular and Extracellular Microenvironment on the Same Formalin-Fixed Paraffin-Embedded Tissue Section

Same-tissue section multimodal imaging is a powerful strategy that spatially profiles tissue histology, cell populations and molecular composition while maximizing tissue economy, preserving spatial molecular relationships, and increasing co-registration capacity. However, performing multiple modalities on the same tissue section can destroy or chemically alter the tissue, compromising downstream data. Here, we systematically assess integration of picrosirius red staining, hematoxylin and eosin staining, and multiplexed immunofluorescence into N-glycan and extracellular matrix peptide matrix-assisted laser/desorption ionization imaging mass spectrometry (IMS) workflows. We evaluate alterations in tissue morphology, stain efficiency, IMS feature intensity as well as IMS feature localization after upstream modality integration. We propose an optimized multimodal sequence that maximizes data quality and follows a very specific order of: autofluorescence microscopy, multiplexed immunofluorescence, picrosirius red staining, N-glycan IMS, hematoxylin and eosin staining, and extracellular matrix peptide IMS. Overall, this work develops an optimized multimodal workflow that comprehensively images tissue morphology, collagen fibers, and cell populations at single-cell resolution as well as multiplexed N-glycan composition and multiplexed extracellular matrix peptides with post-translational modification status from a single tissue section.

biochemistry↗

bioRxiv2026

Multimodal Molecular Mapping of the Vasculature in Human Cortex Reveals Lipid Markers of Cerebral Amyloid Angiopathy

Cerebral amyloid angiopathy (CAA) commonly co-occurs with Alzheimers disease (AD), yet the molecular changes that accompany vascular {beta}-amyloid deposition in human tissue remain incompletely defined. Herein, we use a novel imaging approach that combines matrix-assisted laser desorption/ionization imaging mass spectrometry (IMS) with immunofluorescence microscopy on the same sections of postmortem human frontal cortex to map the lipid microenvironment of leptomeningeal vasculature in cases with and without CAA. Autofluorescence-guided regions-of-interest were imaged by IMS in both negative and positive ion modes and registered to post-IMS-acquired microscopy images. Immunofluorescence microscopy using collagen IV, -smooth muscle actin (SMA), and thiazine red enabled automated segmentation of total, amyloidpositive, and amyloid-negative vasculature regions. A CAA index, the ratio of amyloid-positive area to total vasculature area in a region imaged by IMS, was used to define vasculature and classify each case into having CAA, or CAA-present and not having CAA, or CAA-absent. An interpretable machine learning approach (XGBoost models with Shapley additive explanations for interpretation) was trained on pixel-level spectra and identified lipid signatures of vascular identity shared across groups as well as class-specific marker candidates that distinguished CAA-present from CAA-absent vasculature. CAA-present vessels were enriched for gangliosides (e.g., GM1), whereas CAA-absent vessels were characterized by higher contributions from phosphatidylserines (e.g., long-chain polyunsaturated PS species). Univariate differences were inconsistent between the two groups, but multivariate models in negative mode yielded stable discriminatory features. These results define spatial lipid correlates of vascular amyloid pathology in the human brain and establish a multimodal framework for mechanistically linking lipid metabolism, vascular integrity, and CAA in AD.

neuroscience↗

bioRxiv2025

A Multimodal Imaging Pipeline for the Discovery of Molecular Markers of Cellular Neighborhoods

Insights into tissue microenvironments are constrained by profiling cellular and molecular components independently. To address this, we developed an integrated, multimodal workflow combining imaging mass spectrometry and highly multiplexed immunofluorescence on the same sample. Custom computational pipelines enable precise spatial co-registration, facilitating direct integration of cellular and molecular profiles. CODEX-derived cellular and neighborhood masks enable mining of IMS-derived lipid data to identify molecular markers of cell types and spatial neighborhoods in human kidney tissue. We discovered distinct carnitine distributions in cortical and medullary regions, indicating metabolic heterogeneity driven by microenvironment-specific oxygen levels and energy demands. Glomerular cell-type-specific analysis found ether-linked phosphatidylcholine and sphingomyelin, species associated with slit diaphragm integrity, localized to podocytes. Immune cell neighborhoods exhibited molecular signatures consistent with cell signaling and activation pathways in damaged tissue regions. This multi-omic framework links cellular organization with molecular signatures to unveil cellular and molecular relationships underlying tissue function and pathology.

molecular biology↗

bioRxiv2024

Revealing In Situ Molecular Profiles of Glomerular Cell Types and Substructures with Integrated Imaging Mass Spectrometry and Multiplexed Immunofluorescence Microscopy

Glomeruli filter blood through the coordination of podocytes, mesangial cells, fenestrated endothelial cells, and the glomerular basement membrane. Cellular changes, such as podocyte loss, are associated with pathologies like diabetic kidney disease (DKD). However, little is known regarding the in situ molecular profiles of specific cell types and how these profiles change with disease. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is well-suited for untargeted tissue mapping of a wide range of molecular classes. Additional imaging modalities can be integrated with MALDI IMS to associate these biomolecular distributions to specific cell types. Herein, we demonstrate an integrated workflow combining MALDI IMS and multiplexed immunofluorescence (MxIF) microscopy. High spatial resolution MALDI IMS (5 {micro}m pixel size) was used to determine lipid distributions within human glomeruli, revealing intra-glomerular lipid heterogeneity. Mass spectrometric data were linked to specific glomerular cell types through new methods that enable MxIF microscopy to be performed on the same tissue section following MALDI IMS without sacrificing signal quality from either modality. A combination of machine-learning approaches was assembled, enabling cell-type segmentation and identification based on MxIF data followed by the mining of cell type or cluster-associated MALDI IMS signatures using classification models and interpretable machine learning. This allowed the automated discovery of spatially specific biomarker candidates for glomerular substructures and cell types. Overall, the work presented here establishes a toolbox for probing molecular signatures of glomerular cell types and substructures within tissue microenvironments and provides a framework that applies to other kidney tissue features and organ systems.

biochemistry↗

bioRxiv2023

In situ lipidomics of Staphylococcus aureus osteomyelitis using imaging mass spectrometry

Osteomyelitis occurs when Staphylococcus aureus invades the bone microenvironment, resulting in a bone marrow abscess with a spatially defined architecture of cells and biomolecules. Imaging mass spectrometry and microscopy are invaluable tools that can be employed to interrogate the lipidome of S. aureus-infected murine femurs to reveal metabolic and signaling consequences of infection. Here, nearly 250 lipids were spatially mapped to healthy and infection-associated morphological features throughout the femur, establishing composition profiles for tissue types. Ether lipids and arachidonoyl lipids were significantly altered between cells and tissue structures in abscesses, suggesting their roles in abscess formation and inflammatory signaling. Sterols, triglycerides, bis(monoacylglycero)phosphates, and gangliosides possessed ring-like distributions throughout the abscess, indicating dysregulated lipid metabolism in a subpopulation of leukocytes that cannot be discerned with traditional microscopy. These data provide chemical insight into the signaling function and metabolism of cells in the fibrotic border of abscesses, likely characteristic of lipid-laden macrophages.

biochemistry↗

bioRxiv2022

A multiscale atlas of the molecular and cellular architecture of the human kidney

Tissue atlases provide foundational knowledge on the cellular organization and molecular distributions across molecular classes and spatial scales. Here, we construct a comprehensive spatio-molecular lipid atlas of the human kidney from 29 donor tissues using integrated multimodal molecular imaging. Our approach leverages high spatial resolution matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) for untargeted lipid mapping, stained microscopy for histopathological assessment, and tissue segmentation using autofluorescence microscopy. With a combination of unsupervised, supervised, and interpretive machine learning, the atlas provides multivariate lipid profiles of specific multicellular functional tissue units (FTUs) of the nephron, including the glomerulus, proximal tubules, thick ascending limb, distal tubules, and collecting ducts. In total, the atlas consists of tens of thousands of FTUs and millions of mass spectrometry measurements. Detailed patient, clinical, and histopathologic information allowed molecular data to be mined based on these features. As examples, we highlight the discovery of how lipid profiles are altered with sex and differences in body mass index.

biochemistry↗

bioRxiv2020

Elevated dietary ω-6 polyunsaturated fatty acids induce reversible peripheral nerve dysfunction that exacerbates comorbid pain conditions

Chronic pain is the leading cause of disability worldwide1 and commonly associated with comorbid disorders2. However, the role of diet in chronic pain is poorly understood. Of particular interest is the Western-style diet, enriched with {omega}-6 polyunsaturated fatty acids (PUFAs) that accumulate in membrane phospholipids and oxidize into pronociceptive oxylipins3,4. Here we report that mice administered a diet enriched with {omega}-6 PUFAs develop persistent nociceptive hypersensitivities, spontaneously-active and hyper-responsive glabrous afferent fibers, and histologic markers of peripheral nerve damage reminiscent of a peripheral neuropathy. Linoleic and arachidonic acids accumulate in lumbar dorsal root ganglia, with increased liberation via elevated PLA2 activity. Pharmacological and molecular inhibition of PLA2g7 or diet reversal with high {omega}-3 PUFAs attenuate nociceptive behaviors, neurophysiologic abnormalities, and afferent histopathology induced by high {omega}-6 intake. In addition, {omega}-6 accumulation exacerbates the intensity or duration of allodynia observed in preclinical inflammatory and neuropathic pain models, as well as in clinical diabetic neuropathy. Collectively, these data reveal diet as a novel etiology of peripheral neuropathy and risk factor for chronic pain, and implicate multiple therapeutic considerations for clinical pain management.

neuroscience↗