Rationale: The contributions of diverse cell populations in the human lung to pulmonary fibrosis pathogenesis are poorly understood. Single-cell RNA sequencing can reveal changes within individual cell populations during pulmonary fibrosis that are important for disease pathogenesis. Objectives: To determine whether single-cell RNA sequencing can reveal disease-related heterogeneity within alveolar macrophages, epithelial cells, or other cell types in lung tissue from subjects with pulmonary fibrosis compared with control subjects. Methods: We performed single-cell RNA sequencing on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and on one bronchoscopic cryobiospy sample from a patient with idiopathic pulmonary fibrosis. We validated these data using in situ RNA hybridization, immunohistochemistry, and bulk RNA-sequencing on flow-sorted cells from 22 additional subjects. Measurements and Main Results: We identified a distinct, novel population of profibrotic alveolar macrophages exclusively in patients with fibrosis. Within epithelial cells, the expression of genes involved in Wnt secretion and response was restricted to nonoverlapping cells. We identified rare cell populations including airway stem cells and senescent cells emerging during pulmonary fibrosis. We developed a web-based tool to explore these data. Conclusions: We generated a single-cell atlas of pulmonary fibrosis. Using this atlas, we demonstrated heterogeneity within alveolar macrophages and epithelial cells from subjects with pulmonary fibrosis. These results support the feasibility of discovery-based approaches using next-generation sequencing technologies to identify signaling pathways for targeting in the development of personalized therapies for patients with pulmonary fibrosis.

Misharin et al. elucidate the fate and function of monocyte-derived alveolar macrophages during the course of pulmonary fibrosis. These cells persisted throughout the life span, were enriched for the expression of profibrotic genes, and their genetic ablation ameliorated development of pulmonary fibrosis.

Recombinant vesicular stomatitis virus (VSV) vectors expressing homologous filoviral glycoproteins cancompletely protect rhesus monkeys against Marburg virus when administered after exposure and can partially protect macaques after challenge with Zaire ebolavirus. Here, we administered a VSV vector expressing the Sudan ebolavirus (SEBOV) glycoprotein to four rhesus macaques shortly after exposure to SEBOV. All four animals survived SEBOV challenge, while a control animal that received a nonspecific vector developed fulminant SEBOV hemorrhagic fever and succumbed. This is the first demonstration of complete postexposure protection against an Ebola virus in nonhuman primates and provides further evidence that postexposure vaccination may have utility in treating exposures to filoviruses.The filoviruses, Ebola virus (EBOV) and Marburg virus (MARV), cause severe and often fatal infections in humans and nonhuman primates. While there is a single species of MARV, there are four recognized species of EBOV: Ivory Coast ebolavirus (also known as Cote d'Ivoire ebolavirus), Reston ebolavirus, Sudan ebolavirus (SEBOV), and Zaire ebolavirus (ZEBOV) (7,17). Until recently, nearly all EBOV outbreaks in humans have been caused by either SEBOV or ZEBOV. A possible fifth species of EBOV was associated with an outbreak in Uganda late in 2007, but little information is available regarding this new EBOV (1). Since 1976, there have been at least 10 outbreaks of ZEBOV, with case fatality rates approaching 90% (17). During the same period, there have been four outbreaks of SEBOV with mortality rates of approximately 50% (17).Remarkable progress has been made over the last few years in developing candidate preventive vaccines that can protect nonhuman primates against EBOV and MARV (2,3,14,15,[18][19][20][21]. Advances in development of postexposure treatments and therapies against the filoviruses have been much slower. Some degree of success has been achieved using strategies that mitigate the coagulation abnormalities that characterize filoviral infection (10,11,13). Several new postexposure treatment approaches based on small interfering RNA (12) and antisense oligomers (6, 22) have shown promising results in rodent models, but there have been no published reports of either treatment strategy being evaluated in the more stringent macaque models. Recently, we showed the first complete postexposure protection of nonhuman primates against a filovirus by administering a live-attenuated recombinant vesicular stomatitis virus (rVSV) vector expressing the MARV glycoprotein (GP) shortly after a high-dose MARV challenge (4). We subsequently demonstrated that an rVSV vector expressing the ZEBOV GP protected 50% of rhesus macaques when admin-* Corresponding author. Mailing address:

For Ebola virus (EBOV), 4 different species are known: Zaire, Sudan, Côte d'Ivoire, and Reston ebolavirus. The newly discovered Bundibugyo ebolavirus has been proposed as a 5th species. So far, no cross-neutralization among EBOV species has been described, aggravating progress toward cross-species protective vaccines. With the use of recombinant vesicular stomatitis virus (rVSV)-based vaccines, guinea pigs could be protected against Zaire ebolavirus (ZEBOV) infection only when immunized with a vector expressing the homologous, but not a heterologous, EBOV glycoprotein (GP). However, infection of guinea pigs with nonadapted wild-type strains of the different species resulted in full protection of all animals against subsequent challenge with guinea pig-adapted ZEBOV, showing that cross-species protection is possible. New vectors were generated that contain EBOV viral protein 40 (VP40) or EBOV nucleoprotein (NP) as a second antigen expressed by the same rVSV vector that encodes the heterologous GP. After applying a 2-dose immunization approach, we observed an improved cross-protection rate, with 5 of 6 guinea pigs surviving the lethal ZEBOV challenge if vaccinated with rVSV-expressing SEBOV-GP and -VP40. Our data demonstrate that cross-protection between the EBOV species can be achieved, although EBOV-GP alone cannot induce the required immune response.