No abstract

Summary Polymeric substances produced by microbes play a key role for the development of soil aggregates. Here, we investigated the dynamics of bacterial families contributing to the formation of exopolysaccharides and lipopolysaccharides, major constituents of polymeric substances, at a managed land reclamation site of a post‐mining area. We collected soil samples from the initial and the agricultural management phase and expected a peak in the abundance of bacteria capable for exopolysaccharide and lipopolysaccharide production at the points of the biggest disturbances. We used shotgun metagenomic sequencing in combination with measurements of exopolysaccharide concentrations. Our results underline the importance of exopolysaccharide and lipopolysaccharide‐producing bacteria after nutrient input combined with structural disturbance events, caused here by the initial planting of alfalfa and the introduction of a tillage regime together with organic fertilization in the agricultural management phase. Moreover, the changes in management caused a shift in the exopolysaccharide/lipopolysaccharide‐producing community. The initial phase was dominated by typical colonizers of oligotrophic environments, specifically nitrogen fixers (Rhizobiaceae, Comamonadaceae, Hyphomicrobiaceae), while bacteria common in agricultural soils, such as Sphingomonadaceae, Oxalobacteraceae and Nitrospiraceae, prevailed in the agricultural management phase.

Background Small cell lung cancer (SCLC) is generally known to exclude immune cells and durable responses to immunotherapies are rare. Only very few biomarkers to inform immuno-oncology (IO) treatments are established in clinical practice thus far. Recently, four major SCLC subtypes (SCLC-A, SCLC-N, SCLC-P and SCLC-I) were described. Whereas the first three are characterized by activation of specific transcription factors, the SCLC-I (inflamed) subtype is characterized by an inflamed gene signature, high expression of MHC class I (MHC-I) antigen presentation and shows the greatest benefit from addition of immunotherapy to chemotherapy treatment [1,2]. Importantly, MHC-I is epigenetically silenced in the vast majority of SCLC and the presence of MHC-I could serve as a biomarker for the identification of SCLC-I cases. [2]. Here, we aimed to assess the biology of MHC-I high SCLC cases to investigate its role as a biomarker to inform cancer immunotherapies. Methods We combined the power of artificial intelligence (AI)driven computational pathology with multiplex immunofluorescence (mIF) to gain critical insight into the tumor microenvironment (TME) of SCLC. 125 SCLC formalin-fixed, paraffinembedded tissue samples were stained with a mIF panel consisting of six markers: PanCK, CD8, CD68, PD-1, PD-L1, and Ki67. We assessed the phenotype and spatial location of each cell in the pathologist-annotated tumor center and within the AI-segmented stroma and tumor epithelium. Pathologists classified immunohistochemically stained MHC-I slides from the same tissue blocks as MHC-I high, medium, or low according to their H-scores (low: £30; medium: 31-139; high: !140). TME characteristics between those groups were compared. Results In all measured regions, we found higher densities of CD8+ and particularly PD-1/CD8 double positive T-cells in the MHC-I high group. Moreover, we observed the highest proportion of PD-1 positivity among cytotoxic T-cells in the tumor epithelium of MHC-I high samples, which also showed a high density of PD-L1+ tumor cells. Average distance of PD-1+ T-cells to their nearest tumor cell was lowest in the MHC-I high group. In the same group, an average of 19.3% of tumor cells in the epithelium had at least one PD-1+ Tcell within a 50 mm radius, while in the MHC-I low group this average was only 8.9%. Conclusions We utilized cutting-edge computational pathology to establish MHC-I as orchestrator of the composition and spatial arrangement of an inflamed SCLC TME. Beyond that, our findings corroborate the role of MHC-I as a potential biomarker for inflamed SCLC cases, which benefit most from cancer immunotherapies.