Table 2 Ciliary phenotypes associated with mutation in the known PCD genes Encoded protein Ultrastructural defect Defect of function References Dynein intermediate chain 1 Lack of ODA 42 Genes DNAI1 X-linked RPGR TXNDC3 DNAI2 RSPH9 RSPH4A KTU DNAH5 Dynein heavy chain 5 DNAH11 Dynein heavy chain 11 Retinitis pigmentosa guanosine triphosphatase regulator Thioredoxin–nucleoside diphosphate kinase Dynein intermediate chain 2 Radial spoke protein Radial spoke protein Kintoun—involved in the preassembly of dynein arm complexes Lack of ODA No defect Complex defect (dynein arms, central MT) Partial lack of ODA Lack of ODA Lack of central MT pair Lack of central MT pair Partial or full lack of ODA and IDA widely accepted as a diagnostic tool, does not always allow for firm PCD diagnosis and discrimination between PCD and SCD. Similarly, a singular observation of the abnormal CBF or beat pattern in the material obtained from the patient also does not provide an ultimate proof that the disease is attributable to the genetic rather than environmental causes. To differentiate congenital genetic defects from acquired abnormalities that are focal and transient, the presence of the defect should be demonstrated in different areas of the respiratory tract and in specimens sampled at different times (Pifferi et al. 2001); it requires repeated sampling of the mucosa from the patient. Alternatively, a similar effect can be achieved through culturing the respiratory epithelial cells in vitro, to allow the regeneration of the cilia in a controlled environment, free of the agents inducing SCD. In vitro cell cultures of the ciliated cells from the RE The culturing of differentiated cells and tissues derived from the human RE seems to be the best solution both for the differential diagnosis of PCD and SCD and for studies of genotype–phenotype relations in genes involved in the ciliary dysfunction. In addition, it may also be used for the research on ciliogenesis, in studies on drug development and administration, and on the influence of pollutants and pathogens on the functioning of the RE (Jorissen et al. 1991; Dimova et al. 2005; Wilson et al. 1992). Source tissues The informed choice of the source tissue used to initiate pri- mary cultures of the ciliated cells requires good knowledge of J Appl Genetics (2011) 52:39–51 Immotile cilia Immotile cilia Reduced bending capacity, hyperkinetic beat Immotile and motile cilia Pennarun et al. 1999; Guichard et al. 2001; Zariwala et al. 2001, 2006; Failly et al. 2008 Olbrich et al. 2006; Hornef et al. 2006; Failly et al. 2009 Bartoloni et al. 2002; Schwabe et al. 2008 Moore et al. 2006 Partially immotile cilia Duriez et al. 2007 Not known Immotile cilia Immotile cilia Immotile Loges et al. 2008 Castleman et al. 2009 Castleman et al. 2009 Omran et al. 2008 the localization and structure of the RE (Fig. 2a). Basement membrane composed of several types of extracellular matrix (ECM) molecules (Fanucchi et al. 1999), together with the RE, forms the continuous layer of mucous membranes (mucosa), which line the main conducting airways from the nasal cavity, through the trachea down to the bronchial tree. The RE is composed of four types of cells: ciliated columnar cells with hundreds of cilia on their apical side, non-ciliated columnar cells with microvilli, mucous- producing goblet cells, and, the least numerous, small basal cells (Fig. 2b) (Schmidt et al. 1998; Crystal et al. 2008; Jones 2001). While the arrangement of cell nuclei in the RE suggests its multi-layered organization, all four cell types grow in one layer, contacting the basement membrane; the RE is, therefore, often referred to as pseudostratified epithelium (Schmidt et al. 1998). Basal cells, which rest in the deeper layers of the RE and do not reach the airway lumen (Crystal et al. 2008), are anchored to the basement membrane by the use of hemi- desmosomes. Goblet and columnar (ciliated and non- ciliated) cells contact the basement membrane only by cell-adhesion molecules (Mygind and Dahl 1998), but they also form tight contacts with the adjacent basal cells (Mygind and Dahl 1998). Basal cells are the stem cells of the pseudostratified zone (Crystal et al. 2008), and they are responsible for the growth of the RE and its regeneration after injury (Rock et al. 2009). Although basal cells have the highest division potential, columnar cells can also divide (Randell 2006). In addition, columnar cells can ‘transdifferentiate’ into all of the remaining cell types without dividing themselves (Randell 2006). The relative contribution of goblet and ciliary cells in the composition of healthy pseudostratified epithelium is not