Highlights d Systematic identification of colon cancer-associated proteins and phosphosites d Proteomics-supported neoantigens and cancer/testis antigens in 78% of the tumors d Rb phosphorylation is an oncogenic driver and a putative target in colon cancer d Glycolysis inhibition may render MSI tumors more sensitive to checkpoint blockade

Highlights d Proteogenomics characterization of 218 pediatric brain tumor samples of 7 histologies d Proteomic clusters reveal actionable biological features spanning histological boundaries d Proteomics reveal downstream effects of DNA alterations not evident in transcriptomics d Kinase activity analyses provide insights into pathway activities and druggable targets

Highlights d Unsupervised clustering revealed subtype with EMT and phosphoprotein signatures d Potential therapeutic vulnerabilities included survivin, NSD3, LSD1, and EZH2 d Rb phosphorylation nominated as a biomarker for trials with CDK4/6 inhibitors d Detailed immune landscape analysis highlighted targetable points of immuneregulation

Objective Heightened inflammation, dysregulated immunity, and thrombotic events are characteristic of hospitalized COVID‐19 patients. Given that platelets are key regulators of thrombosis, inflammation, and immunity they represent prime candidates as mediators of COVID‐19‐associated pathogenesis. The objective of this study was to understand the contribution of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) to the platelet phenotype via phenotypic (activation, aggregation) and transcriptomic characterization. Approach and Results In a cohort of 3915 hospitalized COVID‐19 patients, we analyzed blood platelet indices collected at hospital admission. Following adjustment for demographics, clinical risk factors, medication, and biomarkers of inflammation and thrombosis, we find platelet count, size, and immaturity are associated with increased critical illness and all‐cause mortality. Bone marrow, lung tissue, and blood from COVID‐19 patients revealed the presence of SARS‐CoV‐2 virions in megakaryocytes and platelets. Characterization of COVID‐19 platelets found them to be hyperreactive (increased aggregation, and expression of P‐selectin and CD40) and to have a distinct transcriptomic profile characteristic of prothrombotic large and immature platelets. In vitro mechanistic studies highlight that the interaction of SARS‐CoV‐2 with megakaryocytes alters the platelet transcriptome, and its effects are distinct from the coronavirus responsible for the common cold (CoV‐OC43). Conclusions Platelet count, size, and maturity associate with increased critical illness and all‐cause mortality among hospitalized COVID‐19 patients. Profiling tissues and blood from COVID‐19 patients revealed that SARS‐CoV‐2 virions enter megakaryocytes and platelets and associate with alterations to the platelet transcriptome and activation profile.

Highlights d Proteomics and glycoproteomics of 83 ovarian cancer and 23 relevant non-tumor tissues d Glycosylation is associated with three tumor clusters d Tumor-specific changes of glycoproteins and glycosites are apparent d Enzymes responsible for the glycosylation alterations are identified

Given the evidence for a hyperactive platelet phenotype in COVID-19, we investigated effector cell properties of COVID-19 platelets on endothelial cells (ECs). Integration of EC and platelet RNA sequencing revealed that plateletreleased factors in COVID-19 promote an inflammatory hypercoagulable endotheliopathy. We identified S100A8 and S100A9 as transcripts enriched in COVID-19 platelets and were induced by megakaryocyte infection with SARS-CoV-2. Consistent with increased gene expression, the heterodimer protein product of S100A8/A9, myeloidrelated protein (MRP) 8/14, was released to a greater extent by platelets from COVID-19 patients relative to controls. We demonstrate that platelet-derived MRP8/14 activates ECs, promotes an inflammatory hypercoagulable phenotype, and is a significant contributor to poor clinical outcomes in COVID-19 patients. Last, we present evidence that targeting platelet P2Y 12 represents a promising candidate to reduce proinflammatory platelet-endothelial interactions. Together, these findings demonstrate a previously unappreciated role for platelets and their activationinduced endotheliopathy in COVID-19.

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32The immune systems of free-living mammals such as humans and wild mice display a 33 heightened degree of activation compared with laboratory mice maintained under artificial 34 conditions. Here, we demonstrate that releasing inbred laboratory mice into an outdoor enclosure 35to mimic life in a natural environment alters the state of immunity. In addition to enhancing the 36 differentiation of T cell populations previously associated with pathogen exposure, we found that 37 outdoor release of mice led to an increase in circulating granulocytes. However, rewilded mice 38 were not infected by pathogens previously implicated in immune activation. Rather, changes to 39 the immune system were associated with an altered composition of the microbiota, and fungi 40 isolated from rewilded mice were sufficient to increase circulating granulocytes. These findings 41 establish an experimental procedure to investigate the impact of the natural environment on 42 immune development and identify a role for sustained fungal exposure in determining 43 granulocyte numbers. 44 45 46 48 research and has enabled fundamental advances in basic immunology. Yet, this ubiquitous model 49 fails to recreate certain aspects of human immunity. Inbred laboratory mice and adult humans 50 differ in the proportion of leukocyte subsets, transcriptional responses to microbial challenges, 51 and other immune parameters (Masopust et al., 2017; Tao and Reese, 2017). Such differences 52 may limit the predictive value of experiments with mice when studying complex inflammatory 53 and infectious diseases, resulting in significant shortcomings in translating laboratory 54 observations to humans. 55Recent findings suggest that this shortcoming of the rodent model may be due to the 56 specific pathogen free (SPF) environment in which they are maintained. Wild mice and pet store 57 mice, both of which are exposed to a litany of pathogens that are typically excluded from SPF 58 facilities, display an abundance of differentiated memory T cells that more closely resembles the 59 state of immunity in adult humans (Abolins et al., 2017; Beura et al., 2016; Choi et al., 2019). 60Similarly, transferring embryos from lab mice into wild mice generates commensal-and 61 pathogen-exposed offspring (wildlings) that more faithfully recreate human immunity than 62 standard SPF mice, including the unresponsiveness to immunotherapies that failed in clinical 63 trials (Rosshart et al., 2019). Sequentially infecting SPF mice with 3 viruses and a helminth shifts 64 the gene expression profile of peripheral blood mononuclear cells (PBMCs) towards that of pet 65 store mice and adult humans (Reese et al., 2016), further highlighting the role for pathogen 66 experience in normalizing the immune system. SPF mice are also distinguished from free-living 67 mammals by the lack of exposure to potentially immuno-stimulatory members of the microbiota 68 that are absent in a laboratory animal facility. For example, the offspring of germ-free mice 69 inoculated with ileocecal contents from ...