The University of Vermont College of Medicine and the Vermont Lung Center, with support from the National Heart, Lung, and Blood Institute (NHLBI), the American Thoracic Society, the Alpha-1 Foundation, and the Pulmonary Fibrosis Foundation, convened a workshop, "Stem Cells and Cell Therapies in Lung Biology and Lung Diseases," to review our current understanding of the role of stem and progenitor cells in lung repair after injury and to review the current status of cell therapy approaches for lung diseases. These are rapidly expanding areas of study that both provide further insight into and challenge traditional views of mechanisms of lung repair after injury and pathogenesis of several lung diseases. The goals of the conference were to summarize the current state of the field, discuss and debate current controversies, and to identify future research directions and opportunities for both basic and translational research in cell-based therapies for lung diseases. This workshop was a follow-up to an inaugural workshop held at the University of Vermont in 2005, "Adult Stem Cells, Lung Biology, and Lung Disease," sponsored by the NHLBI and the Cystic Fibrosis Foundation, together with the Vermont Lung Center and the University of Vermont College of Medicine (1). That workshop was instrumental in helping guide research and funding priorities. Since the 2005 workshop, investigations of stem cells and cell therapies in lung biology and diseases have continued to rapidly expand. However, there have been several distinct changes in focus and direction, particularly with respect to cell-based therapy approaches. For example, engraftment of airway or alveolar epithelium by stem or progenitor cells originating from outside of the lung is now viewed to be a rarer occurrence than previously described and of unclear physiologic or therapeutic significance. In contrast, circulating endothelial progenitor cells (EPCs) can contribute to regeneration of diseased pulmonary vasculature and are being investigated in patients with pulmonary hypertension in a clinical trial being conducted at the University of Toronto and in one recently completed at Zhejiang University, China. Circulating EPCs may also play roles in both acute lung injury and in fibrotic lung diseases. Furthermore, increasing evidence suggests that circulating fibrocytes can contribute to the pathophysiology of fibrotic lung diseases and thus may be a potential therapeutic target. In addition, novel areas of investigation have developed that include increasing exploration of three-dimensional culture systems and bioengineering approaches to generate functional lung tissue ex vivo and in vivo. Mesenchymal stem cells (MSCs) have been found to exert profound suppressive effects on immune cells and pathways and have demonstrated both safety and efficacy in phase 1 and 2 trials in immune-mediated diseases such as graft-versus-host disease (GVHD) and Crohn's disease. Recent publications and several abstracts presented at the workshop demonstrate that MSCs suppress lung injury and inflammation in several mouse models of inflammatory and immune-mediated lung diseases. These areas are predicted to be of intense investigation over the next several years. Progress continues to be made in investigations of local (endogenous) stem and progenitor cells resident in the lungs. Further understanding of the identity and lineage expansion properties of previously identified endogenous progenitor populations, including variant Clara cells, bronchoalveolar stem cells (BASCs), and side population cells, suggests an increasingly complex network of cellular repair after injury. Most recently, embryonic origin Oct-4+ Clara cell secretory protein (CCSP+) cells have been identified in neonatal mouse lungs and have been postulated to play a progenitor role in adult lung. However, study of endogenous lung stem and progenitor cells is complicated by the role of specific microenvironmental niches in which these cells reside. Alteration of the niches with experimental protocols or removal of cells from the niches can change their identifying characteristics and biologic activities. One of the challenges facing the field is to devise lineage tracing and other study mechanisms to define, characterize, and explore potential therapeutic and/or pathologic properties of endogenous lung progenitor cells. Notably, the existence of lung cancer stem cells is an area of increasing focus and high interest but remains poorly understood. Another challenge is that most studies of endogenous progenitor cells have used mouse models. Correlative information in human lungs remains poorly defined. Comparably, most studies of exogenous cells in lung repair have used mouse models, with relatively limited data in patient models. A continuing issue of confusion is that of terminology. Precise definitions and characterizations of specific cell populations, notably MSCs and EPCs, are not agreed upon. The terms "stem cell" and "progenitor cell" are still used with varying degrees of clarity and precision by different investigators and in recent publications. This continues to complicate comparison of different investigative approaches. A glossary of relevant working definitions applicable to lung is depicted in Table 1. This glossary does not necessarily reflect an overall consensus for the definition of each term and will undergo continuing revision as overall understanding of the cell types and mechanisms involved in lung repair continues to be elucidated. Nonetheless, it is a useful framework. In the first session, after an overview of the field by Diane Krause (Yale University), respective presentations by Wellington Cardoso (Boston University), Barry Stripp (Duke University), Ivan Bertoncello (Australian Stem Cell Center), and Douglas Ball (Johns Hopkins University School of Medicine) reviewed the current state of knowledge of endogenous stem cell populations and their potential to initiate or augment repair. This included lessons learned from lung development, the role of the local microenvironmental niches, and consideration of lung cancer progenitor cells. Key points made during this session were that stem cells are operationally defined not solely by their intrinsic developmental potential but by their interaction with the permissive or restrictive microenvironments in which they reside. Furthermore, the stem cell niche is a dynamic "temporal" niche with the capacity to modify stem cell behavior/readout in different contexts. Moreover, stem cell-associated markers are not uniquely expressed by stem cells and are unreliable predictors of the stem cell potential of isolated cells, requiring validation by functional assays and lineage-tracing studies, particularly when interrogating isolated cells in which histomorphometric spatial and positional cues are lost. Also included in this session was a presentation by Rick Wetsel (University of Texas) demonstrating that cells with phenotypic characteristics of type 2 alveolar epithelial cells could be derived in vitro from one of the approved human embryonic stem (ES) cell lines without the requirement for an embryoid body intermediate. Although the study of human ES cells has been restricted in the United States, only limited information exists from work in other countries on use of human ES cells for lung repair and regeneration. The second and third sessions highlighted advances in cell therapy approaches for lung diseases and also presented data from clinical trials of cell therapies in other diseases. New and developing areas in bioengineering approaches for cell therapies of lung diseases were explored in the second session. Presentations by Dennis Discher (University of Pennsylvania) and Mingyao Liu (University of Toronto) explored the effects of physical environment and three-dimensional matrices on stem cells and lung regeneration. Dario Fauza (Boston Children's Hospital) demonstrated that amniotic fluid-derived MSCs could be used for tracheal repair. Bethany Moore (University of Michigan) and Kurt Stenmark (University of Colorado Health Sciences Center) reviewed current understanding of the role of fibrocytes in fibrotic lung disease and of EPCs in pulmonary vascular and fibrotic lung diseases, respectively. Finally, Johnny Huard (University of Pittsburgh) presented an update in stem cell trials for muscle diseases. Immunomodulatory effects of stem cells were explored in the third session. Results of a phase 2 clinical trial of MSCs in Crohn's disease were presented by Jane Onken (Duke University School of Medicine) demonstrating both safety and efficacy in otherwise treatment-resistant patients. This was followed by exploration of MSC effects in inflammatory and immune-mediated lung diseases by Donald Phinney (Tulane University) and Daniel Weiss (University of Vermont). Ellen Burnham (University of Colorado Health Sciences Center) and Duncan Stewart (University of Toronto) presented an update on EPCs and initial results from the EPC trial in pulmonary hypertension being conducted at the University of Toronto. Keith March (Indiana University) presented an update on cardiac trials and Donald Fink (U.S. Food and Drug Administration [FDA]) presented a perspective from the FDA. After extensive discussion, both immunomodulation and bioengineering approaches using MSCs and other stem cell populations were identified as areas of high priority for expanding study. In the final session, Alan Michelson (National Institutes of Health [NIH]) discussed a systems-based strategy to cell therapies, and Mike Rosenzweig and John Walsh, respective presidents of the Pulmonary Fibrosis and Alpha-1 Foundations, presented perspectives on stem cell research from the views of nonprofit respiratory disease foundations.