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The spatial distribution of type 1 and type 17 immune transcriptomics profiles in murine models of chronic lung infection by opportunistic pathogens

F Nicola(1) F Di Marco(1,3) F Saliu(1) C Oneto(1) S De Pretis(1) F Giannese(1) D M Cirillo(1) N I Lorè(1,3)

1:San Raffaele Scientific Institute; 2:Universita Vita-Salute San Raffaele; 3:Fondazione Centro San Raffaele

The spatial distribution of local immune responses induced by chronic lung infections was not well characterized. Recently developed technologies allow to determine the local transcriptomic profile associated with inflamed tissues. Here, we exploited Visium spatial technology, and we aim at identifying the transcriptomic profiles and the tissue location of type 1 or type 17 immune response in murine lungs during long-term chronic bacterial infection respectively by Mycobacterium abscessus (Mab) and Pseudomonas aeruginosa (Pa). Visium Spatial Gene Expression was performed from formalin-fixed paraffin-embedded (FFPE) lungs and ended with downstream analyses, such as spot deconvolution, results were validated by FACs/immunochemistry analysis. Lung tissue with chronic Mab infection was characterized by the presence of type 1 immunity and the formation of granuloma-inflated areas. Spatial inflammatory profiles of granuloma areas displayed a high local type 1 immune response in comparison to uninfected tissue, intended as a high proportion of immune cells and proinflammatory gene signatures related to Interferon-signalling and M1 macrophages phenotype. Similarly, the dynamic change in the location of type 17 immune response was observed in inducible bronchus-associated lymphoid tissue (iBalt) and close to the airways in comparison to inflamed areas in chronic Pa infection. These inflammatory profiles were validated by FACS and immunohistochemistry analysis in a second batch of mice. Our data show that spatial transcriptomics technology can be used in the field of host-pathogen interaction to study the spatial distribution of cellular transcriptomic profiles associated with granuloma structures.

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