Marc Claesen

Abstract 802: Multi-omic profiling maps the immune multicellular environment of renal cell carcinoma.

Thao Thanh Thi Tran, Máikel L. Colli, Nathan Heath Patterson, Qanber Raza et autres

Abstract Clear cell renal cell carcinoma (ccRCC) is a biologically heterogeneous malignancy shaped by complex tumor–immune–stromal interactions that drive progression and influence therapeutic response. Despite advances in immunotherapy and combination regimens, many patients exhibit intrinsic or acquired resistance, underscoring the need for …

078 Using Spatial Multi-Omics to Explore Molecular Distributions in Human Skin

Samuele Zoratto, Rehan Haider, Helen Patterson, Wei Zhang et autres

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Multi-omics integration and batch correction using a modality-agnostic deep learning framework

Jose Ignacio Alvira Larizgoitia, Gabriele Partel, Lorenzo Venturelli, Wanqiu Zhang et autres

State-of-the-art biotechnologies allow the detection of different molecular species on the same biological sample, generating complex highly-dimensional multi-modal datasets. Gaining a holistic understanding of biological phenomena, such as oncogenesis or aging, requires integrating these diverse modalities into low-dimensional data representations while correcting …

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Spatial Transcriptomics of Schizophrenia Insular Cortex Reveals Blood-Brain Barrier Hyperglycolysis and Increased Parenchymal Mitochondrial Respiration

Karin Huizer, Vera van Dis, Thao Thanh Thi Tran, Roberto Bakker et autres

Abstract Introduction The blood-brain barrier (BBB) acts as the metabolic and immunological gatekeeper of the brain. Since alterations in neurometabolism and neuroimmunity are found in schizophrenia-spectrum disorders (SSD) which are hypothesised to be important disease mechanisms, we aimed to investigate whether changes …

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91 Using spatial multi-omics to investigate the contribution of tumor microenvironment to minimal residual disease and intrinsic chemoresistance of high-grade serous ovarian cancer

Erin H. Seeley, Basant T. Gamal, Akshay Basi, Heath Patterson et autres

Background Understanding how the abundance, localization, and functional orientation of stromal cells in the tumor microenvironment influences high-grade serous ovarian cancer (HGSC) malignancy and patient survival remains largely unknown. Biomarkers to predict the development of minimal residual disease (MRD) or mechanisms of …

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213 Concordance assessment study of Xenium and Visium spatial transcriptomics assays using multiple carcinoma samples

Elim Cheung, Tong Lu, Lutong Zhang, Wanqiu Zhang et autres

Background The Xenium In Situ platform from 10X Genomics offers sub-cellular resolution for precise spatial transcriptomics study of cellular mechanisms and interactions, while the Visium CytAssist Spatial Gene Expression v2 is a whole transcriptome assay offering 55um resolution. This study assessed the …

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182 Xenium in situ analysis and reproducibility study of multiple carcinomas for clinical studies

Tong Lu, Rikita Gakhar, Elim Cheung, Lutong Zhang et autres

Background 10x Genomics Xenium assay is the newest in situ spatial transcriptomics platform offering sub-cellular resolution in frozen and FFPE tissue sections for a deeper study of cellular mechanisms and interactions. Mapping RNA targets at high specificity with fully customizable assays and …

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832 Reproducibility and quality assessment study of xenium and visium spatial transcriptomics assays from multiple carcinoma samples via an end-to-end spatial multi-omics platform weave

Wanqiu Zhang, Thao Thanh Thi Tran, Alice Ly, B. K. Berger et autres

Background The spatial transcriptomic Xenium platform from 10X Genomics offers sub-cellular resolution for a deeper study of cellular mechanisms and interactions, while the Visium is a 55μm-spatial resolution whole transcriptome assay. This study estimated reproducibility of the Xenium assay and the quality …

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Multimodal MALDI imaging mass spectrometry for improved diagnosis of melanoma

Wanqiu Zhang, Nathan Heath Patterson, Nico Verbeeck, Jessica L. Moore et autres

Imaging mass spectrometry (IMS) provides promising avenues to augment histopathological investigation with rich spatio-molecular information. We have previously developed a classification model to differentiate melanoma from nevi lesions based on IMS protein data, a task that is challenging solely by histopathologic evaluation. …

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Toward Omics-Scale Quantitative Mass Spectrometry Imaging of Lipids in Brain Tissue Using a Multiclass Internal Standard Mixture

Michiel Vandenbosch, Shadrack Mulinge Mutuku, Maria José Q. Mantas, Nathan Heath Patterson et autres

Mass spectrometry imaging (MSI) has accelerated our understanding of lipid metabolism and spatial distribution in tissues and cells. However, few MSI studies have approached lipid imaging quantitatively and those that have focused on a single lipid class. We overcome this limitation by …

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Integration of Multiple Spatial Omics Modalities Reveals Unique Insights into Molecular Heterogeneity of Prostate Cancer

Wanqiu Zhang, Xander Spotbeen, Sebastiaan Vanuytven, Sam Kint et autres

Abstract Recent advances in spatial omics methods are revolutionising biomedical research by enabling detailed molecular analyses of cells and their interactions in their native state. As most technologies capture only a specific type of molecules, there is an unmet need to enable …

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

Michiel Vandenbosch, Shadrack Mulinge Mutuku, Maria José Q. Mantas, Nathan Heath Patterson et autres

Abstract 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 …

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