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Spatial dual host-bacterial gene expression to study pathogenesis and the regulation of virulence factors in tissue during NTM respiratory infections

F Di Marco(1) F Nicola(1) S de Pretis(1) F Giannese(1) F Saliu(1) G Tonon(1) D M Cirillo(1) N I Lorè(1)

1:San Raffaele Scientific Institute

Co-localization of spatial transcriptome information of host and pathogen can improve our understanding of microbial pathogenesis. Here, we aimed to demonstrate that customized bacterial probes can be used to simultaneously identify host-pathogen interactions in formalin-fixed-paraffin-embedded (FFPE) tissues with probe-based spatial transcriptomics technology. Host and bacterial spatial transcriptomics profiles were analyzed exploiting a murine lung tissue chronically infected with agar-embedded Mycobacterium abscessus beads. Customized mycobacterial probes were generated for the constitutively expressed rpoB gene (an RNA polymerase beta subunit) and the virulence factor precursor lsr2, modulated by oxidative stress. Our investigation shed light on significant disparities in host expression profiles between infected and uninfected lung foci. Infected districts displayed the formation of granuloma-like structures accompanied by an upsurge in spatial inflammatory profiles, distinctly characterizing the granulomas and their surroundings. We observed that the rpoB expression correlated with bacterial abundance in the airways, while lsr2 virulence factor showed increased expression in lung tissue with high oxidative stress. Furthermore, the application of a deconvolution step reinforced these observations, unveiling how the diverse host expression landscapes surrounding regions positive for bacteria correlated with distinct immune cellular compositions (e.g proinflammatory macrophages). This observation highlighted a gradient influenced by the proximity to the pathogen signal, underscoring the complex interplay between cellular components and the presence of the pathogen within the tissue environment. Overall, we demonstrate that dual bacterial and host spatial gene expression assay can pave the way for the simultaneous detection of host and bacterial transcriptomes in pathological tissues.

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