Mapping the spatial, cellular, and molecular interactions between host cell and bacteria in tumor tissue reveals a non-random distribution of the intratumoral microbiota that affects cancer progression. NBThighlight
, Schematic showing the experimental approach: RNAscope imaging was implemented to identify tumour areas positive for bacteria orfrom OSCC and CRC tumours embedded in OCT blocks. Tumour tissues were trimmed to fit the capture area on the 10x Visium slide. Following tissue permeabilization, RNA is released from cells and bind to an array of probes that are attached to the surface of the slide within capture spots.
Extended Data Fig. 2 The tumour-associated microbiota resides in highly immunosuppressive microniches with a low proliferation rate., Experimental approach: GeoMx DSP was implemented to assess bacteria-associated microniches in one OSCC DSP cohort and two CRC DSP cohorts . Sequential 4 µm-FFPE slides were prepared to identify spatial bacterial tumour distribution and immunohistochemistry for immune and epithelial compartments on the DSP slide treated with the 77-antibody panel.
Extended Data Fig. 3 The tumour-associated microbiota resides in T-cell-excluded areas, with lower proliferation capabilities., RNAscope-FISH images showing bacteria-positive regions with the corresponding adjacent bacteria-negative region from a OSCC and CRC sample. A sequential IHC slide indicates the staining of CD8, PD-1, PanCK and Ki-67 in Bac+ and Bac- regions from the same tumour samples as it is indicated.
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