Bacteria were first detected in human tumors more than 100 years ago, but the characterization of the tumor microbiome has remained challenging because of its low biomass. We undertook a comprehensive analysis of the tumor microbiome, studying 1526 tumors and their adjacent normal tissues across seven cancer types, including breast, lung, ovary, pancreas, melanoma, bone, and brain tumors. We found that each tumor type has a distinct microbiome composition and that breast cancer has a particularly rich and diverse microbiome. The intratumor bacteria are mostly intracellular and are present in both cancer and immune cells. We also noted correlations between intratumor bacteria or their predicted functions with tumor types and subtypes, patients’ smoking status, and the response to immunotherapy.

Growing evidence suggests that microbes can influence the efficacy of cancer therapies. By studying colon cancer models, we found that bacteria can metabolize the chemotherapeutic drug gemcitabine (2′,2′-difluorodeoxycytidine) into its inactive form, 2′,2′-difluorodeoxyuridine. Metabolism was dependent on the expression of a long isoform of the bacterial enzyme cytidine deaminase (CDDL), seen primarily in Gammaproteobacteria. In a colon cancer mouse model, gemcitabine resistance was induced by intra-tumor Gammaproteobacteria, dependent on bacterial CDDL expression, and abrogated by co-treatment with the antibiotic ciprofloxacin. Gemcitabine is commonly used to treat pancreatic ductal adenocarcinoma (PDAC), and we hypothesized that intra-tumor bacteria might contribute to drug resistance of these tumors. Consistent with this possibility, we found that of the 113 human PDACs that were tested, 86 (76%) were positive for bacteria, mainly Gammaproteobacteria.

Granulocyte colony-stimulating factor (G-CSF) induced hematopoietic stem cell mobilization is widely used for clinical transplantation; however, the mechanism is poorly understood. We report here that G-CSF induced a reduction of the chemokine stromal cell derived factor 1 (SDF-1) and an increase in its receptor CXCR4 in the bone marrow (BM), whereas their protein expression in the blood was less affected. The gradual decrease of BM SDF-1, due mostly to its degradation by neutrophil elastase, correlated with stem cell mobilization. Elastase inhibition reduced both activities. Human and murine stem cell mobilization was inhibited by neutralizing CXCR4 or SDF-1 antibodies, demonstrating SDF-1 CXCR4 signaling in cell egress. We suggest that manipulation of SDF-1 CXCR4 interactions may be a means with which to control the navigation of progenitors between the BM and blood to improve the outcome of clinical stem cell transplantation.

The chemokine stromal-derived factor-1 (SDF-1) controls many aspects of stem cell function. Details of its regulation and sites of production are currently unknown. We report that in the bone marrow, SDF-1 is produced mainly by immature osteoblasts and endothelial cells. Conditioning with DNAdamaging agents (ionizing irradiation, cyclophosphamide, and 5-fluorouracil) caused an increase in SDF-1 expression and in CXCR4-dependent homing and repopulation by human stem cells transplanted into NOD/SCID mice. Our findings suggest that immature osteoblasts and endothelial cells control stem cell homing, retention, and repopulation by secreting SDF-1, which also participates in host defense responses to DNA damage.

IntroductionTransplanted human hematopoietic stem cells must retain specific adhesive capacity to interact with the vascular endothelium that lines the bone marrow (BM) (1-3). The mechanisms by which these cells home to and engraft the BM are still obscure. Murine hematopoietic progenitors (HPCs) have been shown to interact in vivo with both P-selectin and E-selectin on vascular endothelium of murine BM (4). In addition, VCAM-1 has been shown to support rolling of HPC on BM endothelium in the absence of endothelial selectins (4). Nevertheless, optimal recruitment of HPC to the BM requires the combined action of both selectins and VCAM-1 (5). Thus, the initiation of primary rolling adhesion of blood-borne cells to the lining of the BM microvessels under shear flow is critical for the recruitment of HPC to the BM. HPC rolling on BM endothelium is likely to be accompanied by a coordinated sequence of adhesive and activation events leading to cell arrest, a key step in the successful extravasation of blood-borne cells to extravascular beds (6, 7). In these prior studies, the mechanisms by which HPCs develop firm adhesion to BM endothelium in the presence of physiological shear flow have not been elucidated.We recently established a key role for the chemokine SDF-1 and its receptor CXCR4 in murine BM engraftment by human severe combined immunodeficiency (SCID) repopulating stem cells (8). In light of the growing evidence that chemokines can regulate the arrest of leukocytes on blood vessels through integrin-dependent interactions with IgSF ligands, we asked whether SDF-1 regulates CD34 + progenitors interaction with BM endothelium, and if so, how. We now report that human BM endothelium constitutively expresses high levels of SDF-1. Using in vitro flow chamber assays, we have tested the specific effects of SDF-1 on the ability of human cord blood CD34 + progenitors to initiate rolling interactions and arrest on human vascular endothelium and on isolated endothelial receptors, including E-selectin, P-selectin, ICAM-1, and VCAM-1, which have all been shown to be constitutively expressed on both murine and human BM endothelium (9). Our results suggest that SDF-1 is a key player The chemokine SDF-1 plays a central role in the repopulation of the bone marrow (BM) by circulating CD34 + progenitors, but the mechanisms of its action remain obscure. To extravasate to target tissue, a blood-borne cell must arrest firmly on vascular endothelium. Murine hematopoietic progenitors were recently shown in vivo to roll along BM microvessels that display selectins and integrins. We now show that SDF-1 is constitutively expressed by human BM endothelium. In vitro, human CD34 + cells establish efficient rolling on P-selectin, E-selectin, and the CD44 ligand hyaluronic acid under physiological shear flow. ICAM-1 alone did not tether CD34 + cells under flow, but, in the presence of surface-bound SDF-1, CD34 + progenitors rolling on endothelial selectin rapidly developed firm adhesion to the endothelial surface, mediated by an interaction ...