title: Cross-Species Transcriptome Profiling Identifies New Alveolar Epithelial Type I Cell-Specific Genes.
abstract: Diseases involving the distal lung alveolar epithelium include chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma. Accurate labeling of specific cell types is critical for determining the contribution of each to the pathogenesis of these diseases. The distal lung alveolar epithelium is composed of two cell types, alveolar epithelial type 1 (AT1) and type 2 (AT2) cells. Although cell type-specific markers, most prominently surfactant protein C, have allowed detailed lineage tracing studies of AT2 cell differentiation and the cells' roles in disease, studies of AT1 cells have been hampered by a lack of genes with expression unique to AT1 cells. In this study, we performed genome-wide expression profiling of multiple rat organs together with purified rat AT2, AT1, and in vitro differentiated AT1-like cells, resulting in the identification of 54 candidate AT1 cell markers. Cross-referencing with genes up-regulated in human in vitro differentiated AT1-like cells narrowed the potential list to 18 candidate genes. Testing the top four candidate genes at RNA and protein levels revealed GRAM domain 2 (GRAMD2), a protein of unknown function, as highly specific to AT1 cells. RNA sequencing (RNAseq) confirmed that GRAMD2 is transcriptionally silent in human AT2 cells. Immunofluorescence verified that GRAMD2 expression is restricted to the plasma membrane of AT1 cells and is not expressed in bronchial epithelial cells, whereas reverse transcription-polymerase chain reaction confirmed that it is not expressed in endothelial cells. Using GRAMD2 as a new AT1 cell-specific gene will enhance AT1 cell isolation, the investigation of alveolar epithelial cell differentiation potential, and the contribution of AT1 cells to distal lung diseases.
authors.affiliation: Departments of 1 Surgery and.|2 Biochemistry and Molecular Medicine.|3 Norris Comprehensive Cancer Center.
authors.forename: Crystal N
authors.identifier: 0000-0002-8463-7126
authors.initials: CN
authors.lastname: Marconett
authors.affiliation: 3 Norris Comprehensive Cancer Center.|4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and.
authors.forename: Beiyun
authors.identifier: 0000-0002-9084-5933
authors.initials: B
authors.lastname: Zhou
authors.affiliation: 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and.
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Sunohara
authors.affiliation: Departments of 1 Surgery and.|2 Biochemistry and Molecular Medicine.
authors.forename: Tiffany M
authors.initials: TM
authors.lastname: Pouldar
authors.affiliation: 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and.
authors.forename: Hongjun
authors.initials: H
authors.lastname: Wang
authors.affiliation: 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and.
authors.forename: Yixin
authors.initials: Y
authors.lastname: Liu
authors.affiliation: 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and.
authors.forename: Megan E
authors.initials: ME
authors.lastname: Rieger
authors.affiliation: Departments of 1 Surgery and.|2 Biochemistry and Molecular Medicine.|3 Norris Comprehensive Cancer Center.
authors.forename: Evelyn
authors.initials: E
authors.lastname: Tran
authors.affiliation: 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and.
authors.forename: Per
authors.initials: P
authors.lastname: Flodby
authors.affiliation: 5 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.
authors.forename: Kimberly D
authors.initials: KD
authors.lastname: Siegmund
authors.affiliation: 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and.
authors.forename: Edward D
authors.initials: ED
authors.lastname: Crandall
authors.affiliation: Departments of 1 Surgery and.|2 Biochemistry and Molecular Medicine.|3 Norris Comprehensive Cancer Center.
authors.forename: Ite A
authors.initials: IA
authors.lastname: Laird-Offringa
authors.affiliation: 2 Biochemistry and Molecular Medicine.|3 Norris Comprehensive Cancer Center.|4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and.
authors.forename: Zea
authors.identifier: 0000-0001-8673-8177
authors.initials: Z
authors.lastname: Borok
mesh_terms: D056809:Alveolar Epithelial Cells / Q000378:metabolism*; D000818:Animals; D015415:Biomarkers / Q000378:metabolism; D053503:Epithelial Sodium Channels / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity / Q000235:genetics*; D051381:Rats; D015203:Reproducibility of Results; D013045:Species Specificity
chemical_list: D015415:Biomarkers; D053503:Epithelial Sodium Channels
keywords: alveolar epithelium; lung differentiation; microarray analysis; transcriptome analysis; type I cell markers