Highly multiplexed 3D profiling of cell states and immune niches in human tumours

Yapp C, Nirmal AJ, Zhou FY, Wong AYH, Tefft J, Lu YD, Shang Z, Maliga Z, Montero Llopis P, Murphy GF, Lian C, Danuser G, Santagata S, Sorger PK.

Nature Methods. 2025.

Diseases such as cancer involve alterations in cell proportions, states and interactions, as well as complex changes in tissue morphology and architecture. Histopathological diagnosis of disease and most multiplexed spatial profiling relies on inspecting thin (4–5 µm) specimens. Here we describe a high-plex cyclic immunofluorescence method for three-dimensional tissue imaging and use it to show that few, if any, cells are intact in conventional thin tissue sections, reducing the accuracy of cell phenotyping and interaction analysis. However, three-dimensional cyclic immunofluorescence of sections eightfold to tenfold thicker enables accurate morphological assessment of diverse protein markers in intact tumor, immune and stromal cells. Moreover, the high resolution of this confocal approach generates images of cells in a preserved tissue environment at a level of detail previously limited to cell culture. Precise imaging of cell membranes also makes it possible to detect and map cell–cell contacts and juxtracrine signaling complexes in immune cell niches.