Multiplex immunofluorescence-guided laser capture microdissection for spatial transcriptomics of metastatic melanoma tissues

Martínek, Jan; Wu, Te-Chia; Sun, Lili; Lin, Jianan; Kim, Kyung In; Marches, Florentina; Robson, Paul; George, Joshy; Palucka, Karolina

doi:10.1016/j.xpro.2022.101698

Cited by 1 publication

(1 citation statement)

References 10 publications

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“…The catapulted material can be collected, processed further, and subjected to different omics analysis. LMD-coupled RNA sequencing [18][19][20][21] and proteomics [22][23][24][25] allowed the better understanding of the cell type-specific landscape and aided the analysis of spatial organization. In lipidomics (and metabolomics), the acquisition of both in-depth spatial information and comprehensive lipidome coverage is extremely difficult, especially when biological material is limited or lipids are at low abundance [26].…”

Section: Introductionmentioning

confidence: 99%

Development of a Laser Microdissection-Coupled Quantitative Shotgun Lipidomic Method to Uncover Spatial Heterogeneity

Varga-Zsíros

Migh

Marton

et al. 2023

Cells

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Lipid metabolic disturbances are associated with several diseases, such as type 2 diabetes or malignancy. In the last two decades, high-performance mass spectrometry-based lipidomics has emerged as a valuable tool in various fields of biology. However, the evaluation of macroscopic tissue homogenates leaves often undiscovered the differences arising from micron-scale heterogeneity. Therefore, in this work, we developed a novel laser microdissection-coupled shotgun lipidomic platform, which combines quantitative and broad-range lipidome analysis with reasonable spatial resolution. The multistep approach involves the preparation of successive cryosections from tissue samples, cross-referencing of native and stained images, laser microdissection of regions of interest, in situ lipid extraction, and quantitative shotgun lipidomics. We used mouse liver and kidney as well as a 2D cell culture model to validate the novel workflow in terms of extraction efficiency, reproducibility, and linearity of quantification. We established that the limit of dissectible sample area corresponds to about ten cells while maintaining good lipidome coverage. We demonstrate the performance of the method in recognizing tissue heterogeneity on the example of a mouse hippocampus. By providing topological mapping of lipid metabolism, the novel platform might help to uncover region-specific lipidomic alterations in complex samples, including tumors.

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