Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We profiled 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph nodes, using single-cell RNA-seq. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. Despite significant similarity between normal and tumor tissue-resident immune cells, we observed continuous phenotypic expansions specific to the tumor microenvironment. Analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data from 27,000 additional T cells revealed the combinatorial impact of TCR utilization on phenotypic diversity. Our results support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer. Our results have important implications for characterizing tumor-infiltrating immune cells.

Summary Regulatory T (Treg) cells reside in lymphoid organs and barrier tissues where they control different types of inflammatory responses. Treg cells are also found in human cancers, and studies in animal models suggest that they contribute to cancer progression. However, properties of human intratumoral Treg cells and those present in corresponding normal tissue remain largely unknown. Here, we analyzed features of Treg cells in untreated human breast carcinomas, normal mammary gland, and peripheral blood. Tumor-resident Treg cells were potently suppressive and their gene expression pattern resembled that of normal breast tissue, but not of activated peripheral blood Treg cells. Nevertheless, a number of cytokine and chemokine receptor genes, most notably CCR8, were upregulated in tumor-resident Treg cells in comparison to normal tissue resident ones. Our studies suggest that targeting CCR8 for the depletion of tumor-resident Treg cells may represent a promising immunotherapeutic approach for the treatment of breast cancer.

Infection with antibiotic-resistant bacteria, such as vancomycin-resistant Enterococcus (VRE), is a dangerous and costly complication of broad-spectrum antibiotic therapy 1,2 . How antibioticmediated elimination of commensal bacteria promotes infection by antibiotic-resistant bacteria is a fertile area for speculation with few defined mechanisms. Here we demonstrate that antibiotic treatment of mice notably downregulates intestinal expression of RegIIIγ (also known as Reg3g), a secreted C-type lectin that kills Gram-positive bacteria, including VRE. Downregulation of RegIIIγ markedly decreases in vivo killing of VRE in the intestine of antibiotic-treated mice. Stimulation of intestinal Toll-like receptor 4 by oral administration of lipopolysaccharide re-induces RegIIIγ, thereby boosting innate immune resistance of antibiotic-treated mice against VRE. Compromised mucosal innate immune defence, as induced by broad-spectrum antibiotic therapy, can be corrected by selectively stimulating mucosal epithelial Toll-like receptors, providing a potential therapeutic approach to reduce colonization and infection by antibiotic-resistant microbes.Infections caused by highly antibiotic-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA) and VRE, are an increasing menace in hospitalized patients 3,4 . Treatment of serious VRE infections is limited by the paucity of effective antibiotics 5 . VRE colonizes the gastrointestinal tract and it is likely that systemic bloodstream infections are the result of dissemination from the intestine 6 . It has been widely assumed that antibiotic treatment, by eliminating commensal flora, opens intestinal niches and provides increased access to nutrients, thereby enhancing VRE survival and proliferation. Recent studies, however, have demonstrated that commensal microbes in the intestine induce expression of proteins that restrict bacterial survival and growth 7,8 . Thus, whereas commensal microbes may directly restrict VRE proliferation, an alternative hypothesis is that commensal microbes inhibit VRE indirectly by activating mucosal innate immune defenses.Correspondence and requests for materials should be addressed to E.G.P. (Fig. 1b). RegIIIγ is a secreted lectin with potent bactericidal activity against Gram-positive bacteria that is expressed by intestinal epithelial and Paneth cells 7 . Expression of RegIIIγ is dependent on TLR-MyD88-mediated signals in intestinal epithelial cells and is induced by commensal microbes 7,9 . To determine whether RegIIIγ mediates in vivo killing of VRE in the intestine, we injected a blocking polyclonal antiserum 10 against RegIIIγ into ileal loops of wild-type mice before inoculation of VRE. The number of surviving VRE bacteria was increased by over 400% in intestines treated with RegIIIγ-specific antiserum (Fig. 1c), indicating that RegIIIγ mediates in vivo VRE killing.Administration of the broad-spectrum antibiotic combination metronidazole, neomycin and vancomycin (MNV), to which VRE is resistant, markedly increases ...

Accurate identification of tumor-derived somatic variants in plasma circulating cell-free DNA (cfDNA) requires understanding the various biologic compartments contributing to the cfDNA pool. We sought to define the technical feasibility of a high-intensity sequencing assay of cfDNA and matched white-blood cell (WBC) DNA covering a large genomic region (508 genes, 2Mb, >60,000X raw-depth) in a prospective study of 124 metastatic cancer patients, with contemporaneous matched tumor tissue biopsies, and 47 non-cancer controls. The assay displayed a high sensitivity and specificity, allowing for de novo detection of tumor-derived mutations and inference of tumor mutational burden, microsatellite instability, mutational signatures and sources of somatic mutations identified in cfDNA. The vast majority of cfDNA mutations (81.6% in controls and 53.2% in cancer patients) had features consistent with clonal hematopoiesis (CH). This cfDNA sequencing approach revealed that CH constitutes a pervasive biological phenomenon emphasizing the importance of matched cfDNA-WBC sequencing for accurate variant interpretation.