The University of Vermont College of Medicine and the Vermont Lung Center, with support of the National Heart, Lung, and Blood Institute (NHLBI), the Alpha-1 Foundation, the American Thoracic Society, the Emory Center for Respiratory Health, the Lymphangioleiomyomatosis (LAM) Treatment Alliance, and the Pulmonary Fibrosis Foundation, convened a workshop, "Stem Cells and Cell Therapies in Lung Biology and Lung Diseases," held July 26-29, 2009 at the University of Vermont, to review the 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 provide further insight into and challenge traditional views of the 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 identify future research directions and opportunities for both basic and translational research in cell-based therapies for lung diseases. This conference was a follow-up to two previous conferences held at the University of Vermont, "Adult Stem Cells, Lung Biology, and Lung Disease" sponsored by the NHLBI, the Cystic Fibrosis Foundation, the University of Vermont College of Medicine, and the Vermont Lung Center in 2005 and "Stem Cells and Cell Therapies in Lung Biology and Diseases sponsored by the NHLBI, Alpha-1 Foundation, American Thoracic Society, Pulmonary Fibrosis Foundation, University of Vermont College of Medicine, and the Vermont Lung Center in 2007. Those conferences have been instrumental in helping to guide research and funding priorities (1, 2). Since the 2007 conference, investigations of stem cells and cell therapies in lung biology and diseases have continued to expand rapidly. However, there continue to be changes in focus and direction, particularly with respect to cell-based therapy approaches. Recent studies of immunomodulation and paracrine effects of adult stem and progenitor cells, notably adult mesenchymal stromal (stem) cells (MSCs) derived from bone marrow, adipose, and other tissues, have increasingly provided evidence of efficacy in animal models of acute and fibrotic lung injuries as well as in asthma, bronchopulmonary dysplasia, chronic obstructive pulmonary disease (COPD), sepsis, and other lung diseases. Although the mechanisms of MSC effects in these models are not yet fully understood, growing evidence implicates both soluble mediators released by the MSCs as well as cell to cell contact of MSCs with different inflammatory and immune effector cells. These studies have recently been extended to human lung explant models, and it is anticipated that clinical investigations of initial safety and efficacy of MSCs in acute lung injury will occur in the near future. In parallel, a 6-month interim analysis of a current clinical trial in the United States assessing systemic administration of MSCs in patients with moderate to severeCOPDhas demonstrated safety and has yielded promising results with respect to efficacy. This trial has completed its 2-year observation period, and data is expected to be released in late 2010 or early 2011.Circulating endothelial progenitor cells (EPCs) can contribute to regeneration of diseased pulmonary vasculature, and two recent clinical investigations in China have suggested the efficacy of autologous bone marrow-derived EPC administration in both adult and pediatric patients with pulmonary hypertension. A comparable trial of autologous EPC administration in pulmonary hypertension, the Pulmonary Hypertension: Assessment of Cell Therapy (PHaCET) trial, is ongoing in Canada. Circulating endothelial progenitor cells may also play roles in both acute lung injury and in fibrotic lung diseases. Engraftment of systemically or intratracheally administered cells remains a controversial issue. Although most available evidence argues against significant engraftment, publications and abstracts presented at the conference suggest that several newly investigated cell types, including those derived from placental tissues or novel cell populations derived from adult bone marrow, may demonstrate a more robust ability to engraft and participate in lung repair. Further, significant advances continue to be made in novel areas of investigation including increasing exploration of 3-dimensional culture systems and bioengineering approaches to generate functional lung tissue ex vivo and in vivo. This has culminated in the first successful clinical use of a bioengineered trachea. In parallel, several recent reports demonstrate the potential feasibility of using decellularized whole lungs as scaffolds for recellularization and subsequent implantation. These areas are predicted to be of intense investigation over the next several years. Comparably, progress continues in studies of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPS). Several groups have presented protocols for deriving definitive endoderm from either ESCs or iPS cultured in vitro and some have further demonstrated the ability to generate cellswith phenotypicmarkers of type 2 alveolar cells from either mouse or human ESCs. In addition, a recent study demonstrated the potential ability of type 2 alveolar epithelial cells, derived in culture from human embryonic stem cells, to engraft in lung and ameliorate experimentally induced lung injury in a rodent model. Nonetheless, many challenges remain to generating functional lung cells fromeither ESCs or iPS. One potentially fruitful area of investigation derives from the recently demonstrated generation of disease-specific iPS from tissue samples obtained from patients with cystic fibrosis, a-1 antitrypsin deficiency, and other genetic or acquired lung diseases. Significant progress continues to be made in investigations of local (endogenous) stem and progenitor cells residing in the lungs. Advances in lineage-tracing approaches and other techniques have provided important insights into understanding the identity and lineage expansion properties of previously identified putative endogenous progenitor populations and suggest an increasingly complex network of cellular repair after injury. However, the study of endogenous lung stem and progenitor cells remains complicated by the role of the 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 continuing to face the field is to continue to devise more refined lineage tracing and other study mechanisms to define, characterize, and explore potential therapeutic and/or pathologic properties of endogenous lung progenitor cells. This includes studies of lung cancer stem cells, an area of increasing focus and high interest that remains incompletely understood. Another challenge is that most studies of endogenous progenitor cells continue to use mouse models. Correlative information in human lungs remains poorly defined. Acontinuing issue of confusion is that of terminology. Despite suggested guidelines from previous conferences and from other sources, precise definitions and characterizations of specific cell populations, notably the putative endogenous cell populations in the lung as well as mesenchymal stromal cells and endothelial progenitor cells, 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 the comparison of different investigative approaches. A glossary of relevant working definitions applicable to the lung, originally presented in the report of the 2007 conference, is depicted in Table 1. This glossary does not necessarily reflect a consensus for the definition of each term and will undergo continuing revision as an overall understanding of the cell types and mechanisms involved in lung repair continue to be elucidated. Nonetheless, it is a useful framework. The first session, "Endogenous Lung Progenitor Cells/Lung Cancer Stem Cells," following an overview of the field by Paul Simmons (University of Texas) and respective presentations by Susan Reynolds (National Jewish), Ed Morrisey (University of Pennsylvania), Barry Stripp (Duke), Majd Mouded (University of Pittsburgh), and Kerstin Sinkevicius (Boston Children's Hospital), reviewed the current state of knowledge of endogenous progenitor cell populations, mechanisms regulating their behavior, 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 emphasized during this session were that stem cells are operationally defined not solely by their intrinsic developmental potential but by their interaction with the microenvironments in which they reside. Further, 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" or "progenitor" cell potential of isolated cells. Validation by functional assays and lineage-tracing studies, particularly when interrogating isolated cells where histomorphometric spatial and positional cues are lost, are increasingly valid and necessary.