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| Item Type: | Preprint |
|---|---|
| Title: | Integrating UHPLC-MS and MALDI-MSI for spatial nucleoside profiling in FFPE breast cancer: a multimodal molecular pathology framework |
| Creators Name: | Wu, Jierong, Geisberger, Sabrina Y., Mastrobuoni, Guido, Lisek, Kamil, Raimundo, Sandra, Nebrich, Grit, Grzeski, Marta, Rajewsky, Nikolaus, Klauschen, Frederick, Klein, Oliver and Kempa, Stefan |
| Abstract: | Formalin-fixed, paraffin-embedded (FFPE) tissues constitute the primary material for diagnostic pathology and retrospective clinical research, yet their use in metabolomics remains limited due to molecular cross-linking and analyte degradation. Here, we establish a cost-efficient molecular pathology workflow that integrates ultra-high-performance liquid chromatography mass spectrometry (UHPLC-MS) with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to quantify and spatially map nucleosides in FFPE breast cancer tissues. Optimized extraction using methanol yielded nucleoside profiles comparable to fresh-frozen tissues, while MALDI-MSI enabled the spatial visualization of nine nucleosides across distinct histological regions. Several nucleosides including deoxyadenosine and 5-formylcytosine showed strong discriminatory power between tumor stages, revealing progressive metabolic rewiring during breast cancer progression. Finally, spatial nucleoside patterns observed in a murine model were recapitulated in patientderived FFPE tissues, underscoring the translational potential of nucleoside-based spatial metabolomics for clinical research and biomarker discovery. Together, this workflow establishes MALDI-MSI as a powerful and scalable spatial molecular pathology tool for interrogating nucleoside biology in archival breast cancer samples. Following MALDI-MSI, the same FFPE tissue sections can undergo laser capture microdissection, enabling genomic, proteomic, or targeted metabolomic profiling of MSI-defined tumor niches and microenvironmental regions. This integration directly links spatial nucleoside signatures to molecular alterations relevant to precision oncology in future. |
| Keywords: | FFPE, UHPLC-MS, MALDI-MSI, Nucleosides, Breast Cancer, Animals, Mice |
| Source: | bioRxiv |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Article Number: | 2026.01.28.701949 |
| Date: | 30 January 2026 |
| Official Publication: | https://doi.org/10.64898/2026.01.28.701949 |
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