Dimitri Sidiropoulos

TL;DR: BugBase is presented, an algorithm that predicts organism-level coverage of functional pathways as well as biologically interpretable phenotypes such as oxygen tolerance, Gram staining and pathogenic potential, within complex microbiomes using either whole-genome shotgun or marker gene sequencing data.

TL;DR: Assessment of FMT to reverse antibiotic- and chemotherapy-induced gut dysbiosis in a mouse model found that FMT can ameliorate these effects and that chemotherapy led to a critical decrease in key ‘health-promoting’ species and to an altered functional profile.

TL;DR: A novel FFPE spatial transcriptomics analysis pipeline is developed to profile the heterogeneous CAF and malignant epithelial cells in PanINs, premalignant lesions that can progress to invasive PDAC.

TL;DR: Overall, this in-depth analysis suggests that entinostat-induced changes on multiple myeloid cell types reduce immunosuppression and increase anti-tumor responses, which, in turn, improve sensitivity to ICIs.

TL;DR: This work established PDO-CAF co-cultures to model tumor cell interactions and validated discoveries using transfer learning into a single-cell RNA-seq atlas of PDAC tumors, culminating in a gene expression pattern of inflammatory processes in epithelial tumor cells.