@article {69854,
	title = {Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment.},
	journal = {Cell Syst},
	year = {2025},
	month = {2025 Apr 09},
	pages = {101261},
	abstract = {<p>Tumors are complex ecosystems composed of malignant and non-malignant cells embedded in a dynamic extracellular matrix (ECM). In the tumor microenvironment, molecular phenotypes are controlled by cell-cell and ECM interactions in 3D cellular neighborhoods (CNs). While their inhibition can impede tumor progression, routine molecular tumor profiling fails to capture cellular interactions. Single-cell spatial transcriptomics (ST) maps receptor-ligand interactions but usually remains limited to 2D tissue sections and lacks ECM readouts. Here, we integrate 3D ST with ECM imaging in serial sections from one clinical lung carcinoma to systematically quantify molecular states, cell-cell interactions, and ECM remodeling in CN. Our integrative analysis pinpointed known immune escape and tumor invasion mechanisms, revealing several druggable drivers of tumor progression in the patient under study. This proof-of-principle study highlights the potential of in-depth CN profiling in routine clinical samples to inform microenvironment-directed therapies. A record of this paper{\textquoteright}s transparent peer review process is included in the supplemental information.</p>
},
	issn = {2405-4720},
	doi = {10.1016/j.cels.2025.101261},
	url = {https://doi.org10.1016/j.cels.2025.101261},
	author = {Pentimalli, Tancredi Massimo and Schallenberg, Simon and Le{\'o}n-Peri{\~n}{\'a}n, Daniel and Legnini, Ivano and Theurillat, Ilan and Thomas, Gwendolin and Boltengagen, Anastasiya and Fritzsche, Sonja and Nimo, Jose and Ruff, Lukas and Dernbach, Gabriel and Jurmeister, Philipp and Murphy, Sarah and Gregory, Mark T and Liang, Yan and Cordenonsi, Michelangelo and Piccolo, Stefano and Coscia, Fabian and Woehler, Andrew and Karaiskos, Nikos and Klauschen, Frederick and Rajewsky, Nikolaus}
}
@article {69247,
	title = {MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution.},
	journal = {Nature Communincations},
	volume = {15},
	year = {2024},
	month = {2024 Feb 26},
	pages = {1764},
	abstract = {<p>Analyzing immune cell interactions in the bone marrow is vital for understanding hematopoiesis and bone homeostasis. Three-dimensional analysis of the complete, intact bone marrow within the cortex of whole long bones remains a challenge, especially at subcellular resolution. We present a method that stabilizes the marrow and provides subcellular resolution of fluorescent signals throughout the murine femur, enabling identification and spatial characterization of hematopoietic and stromal cell subsets. By combining a pre-processing algorithm for stripe artifact removal with a machine-learning approach, we demonstrate reliable cell segmentation down to the deepest bone marrow regions. This reveals age-related changes in the marrow. It highlights the interaction between CXCR1 cells and the vascular system in homeostasis, in contrast to other myeloid cell types, and reveals their spatial characteristics after injury. The broad applicability of this method will contribute to a better understanding of bone marrow biology.</p>
},
	keywords = {Animals, Bone Marrow, Bone Marrow Cells, Hematopoiesis, Hematopoietic Stem Cells, Mice, Stromal Cells},
	issn = {2041-1723},
	doi = {10.1038/s41467-024-45827-6},
	author = {Mertens, Till Fabian and Liebheit, Alina Tabea and Ehl, Johanna and K{\"o}hler, Ralf and Rakhymzhan, Asylkhan and Woehler, Andrew and Katth{\"a}n, Lukas and Ebel, Gernot and Liublin, Wjatscheslaw and Kasapi, Ana and Triantafyllopoulou, Antigoni and Schulz, Tim Julius and Niesner, Raluca Aura and Hauser, Anja Erika}
}
