Single-cell technologies have revealed the complexity of the tumour immune microenvironment with unparalleled resolution^1–9. Most clinical strategies rely on histopathological stratification of tumour subtypes, yet the spatial context of single-cell phenotypes within these stratified subgroups is poorly understood. Here we apply imaging mass cytometry to characterize the tumour and immunological landscape of samples from 416 patients with lung adenocarcinoma across five histological patterns. We resolve more than 1.6 million cells, enabling spatial analysis of immune lineages and activation states with distinct clinical correlates, including survival. Using deep learning, we can predict with high accuracy those patients who will progress after surgery using a single 1-mm² tumour core, which could be informative for clinical management following surgical resection. Our dataset represents a valuable resource for the non-small cell lung cancer research community and exemplifies the utility of spatial resolution within single-cell analyses. This study also highlights how artificial intelligence can improve our understanding of microenvironmental features that underlie cancer progression and may influence future clinical practice.

Phages and cancer immunity: Gut bacteria are involved in the education of T cell immune responses, and the intestinal ecosystem influences anticancer immunity. Fluckiger et al. report microbial antigens that might cross-react with antigens associated with tumor cells. They found that a type of intestinal bacteria called enterococci harbor a bacteriophage that modulates immune responses. In mouse models, administration of enterococci containing the bacteriophage boosted T cell responses after treatment with chemotherapy or programmed cell death protein 1 (PD-1) blockade. In humans, the presence of the bacteriophage was associated with improved survival after PD-1 immunotherapy. A fraction of human T cells specific for naturally processed melanoma epitopes appeared to be able to recognize microbial peptides. This “molecular mimicry” may represent cross-reactivity between tumors and microbial antigens. Science , this issue p. 936

Background No study has evaluated the predictive and prognostic role of CD8 and PD-L1 coexpression in non–small-cell lung cancer (NSCLC). Methods We analyzed RNA sequencing and/or immunohistochemistry staining in NSCLC patients from The Cancer Genome Atlas (n = 1016), and 34 metastatic NSCLC samples not treated by immunotherapy as prognostic cohorts. As predictive aspect of CD8 and PD-L1, we used 85 NSCLC patients treated with anti-PD-1. Two validation cohorts were used including 44 NSCLC patients treated with anti-PD-1 and an external cohort with different tumor types. Results In prognostic cohorts, high CD8A expression was associated with longer OS (p = 0.02), while high CD274 mRNA was associated with poor prognosis (p = 0.05). In predictive cohort, high CD8 expression and CD8A mRNA were associated with longer progression-free survival (PFS) (p = 0.0002). There was no significant association between PD-L1 expression and PFS while high CD274 mRNA was associated with longer PFS (p = 0.009). A combination of CD8A and CD274 was highly predictive of outcome. These results were confirmed in the validation cohorts. This two-genes signature demonstrated similar results compared to gold standard signatures. Conclusion CD8 represents both a prognostic and predictive factor of outcomes, while PD-L1 share different prognostic and predictive roles.

Meta-analyses suggest that yogurt consumption reduces type 2 diabetes incidence in humans, but the molecular basis of these observations remains unknown. Here we show that dietary yogurt intake preserves whole-body glucose homeostasis and prevents hepatic insulin resistance and liver steatosis in a dietary mouse model of obesity-linked type 2 diabetes. Fecal microbiota transplantation studies reveal that these effects are partly linked to the gut microbiota. We further show that yogurt intake impacts the hepatic metabolome, notably maintaining the levels of branched chain hydroxy acids (BCHA) which correlate with improved metabolic parameters. These metabolites are generated upon milk fermentation and concentrated in yogurt. Remarkably, diet-induced obesity reduces plasma and tissue BCHA levels, and this is partly prevented by dietary yogurt intake. We further show that BCHA improve insulin action on glucose metabolism in liver and muscle cells, identifying BCHA as cell-autonomous metabolic regulators and potential mediators of yogurt’s health effects.

Checkpoint inhibitors directed against programmed death receptor 1 (PD-1) and its ligand (PD-L1) changed the treatment of advanced lung non–small cell carcinomas. The decision to treat patients is influenced by PD-L1 expression by tumor cells, but evidence indicates that this staining is heterogenous within a tumor. As PD-L1 staining is tested mostly on biopsies, false negative results can occur due to sampling issues. The clinical impact of this heterogeneity has not been established. We selected 241 patients who underwent pulmonary resection for adenocarcinoma. Tissue microarrays were constructed with five 1 mm cores representative of the histologic patterns observed in each tumor and stained for PD-L1. For each core, the histologic pattern and the percentage of PD-L1 positive tumor cells were noted. Staining heterogeneity was defined as cases with both positive and negative cores at positivity thresholds of 1%, 10%, and 50% of tumor cells. At the 50% cut-off, 37.8% of patients were PD-L1 positive, whereas 22.4% showed staining heterogeneity. Among patients with 1 negative core, 26.5% also had a positive core and could have been misclassified based on 1 biopsy. Mean staining of PD-L1 was higher in solid (47.9%) and micropapillary (24.2%) patterns and was lower in acinar (14.1%), papillary (3.4%), and lepidic (6.4%) architectures. A significant proportion of patients presented a heterogenous staining for PD-L1. A total of 26.5% of patients negative on 1 core turned out to be positive on another core, which raises the consideration of rebiopsy, in particular when lepidic, acinar, or papillary patterns are observed on a biopsy.

Summary: Background: The severe form of equine asthma is associated with pathological changes of the peripheral airways and pulmonary parenchyma that are only partly described. Also, the relationship between these structural alterations and the percentage of neutrophils found within the airway lumen, assessed by bronchoalveolar lavage fluid ( BALF ) cytology, remains ill‐defined. Objective: To examine the histological lesions associated with equine asthma during disease exacerbation and remission, and their relationship with lung function and BALF neutrophilia. Study design: Observational retrospective study. Methods: Peripheral lung tissues, BALF cytology and lung function data from 61 horses (22 controls, 24 asthma exacerbations and 15 asthma remission) were obtained from an equine pulmonary tissue bank. Two pathologists semi‐quantitatively assessed histological features, including airway wall inflammation, interstitial fibrosis, mucus cell hyperplasia, mucostasis, peribronchiolar metaplasia, presence of granuloma and the overall severity of these lesions. Results: Mucostasis, mucus cell hyperplasia, peribronchiolar metaplasia and interstitial fibrosis were associated with disease exacerbation (P≤0.05), and these changes were all attenuated during remission. Airway wall inflammation was greater in horses with asthma in exacerbation compared with horses with asthma in remission and control horses (P≤0.05). Acute (neutrophilic) airway wall inflammation was more frequently detected in asthmatic cases compared with control horses (P<0.0001) and was associated with BALF neutrophilia >5% in control horses (P = 0.002). The degree of bronchiolar inflammation was higher in asthmatic horses in remission stabled and treated pharmacologically compared with those kept on pasture (P = 0.04). Main limitations: Samples obtained from a convenient cohort of horses were studied. Conclusions: Severely asthmatic horses present parenchymal and peribronchial/peribronchiolar lesions possibly contributing to the obstructive nature of the disease.