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Shin H, Morty RE, Sucre JM, Negretti NM, Markmann M, Hossain H, Krauss-Etschmann S, Dehmel S, Hilgendorff A. Reference genes for the developing mouse lung under consideration of biological, technical and experimental confounders. Sci Rep 2022; 12:17679. [PMID: 36271035 PMCID: PMC9587035 DOI: 10.1038/s41598-022-19071-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/24/2022] [Indexed: 01/18/2023] Open
Abstract
For gene expression analysis, the raw data obtained from RT-qPCR are preferably normalized to reference genes, which should be constantly expressed regardless of experimental conditions. Selection of reference genes is particularly challenging for the developing lung because of the complex transcriptional and epigenetic regulation of genes during organ maturation and injury repair. To date, there are only limited experimental data addressing reliable reference genes for this biological circumstance. In this study, we evaluated reference genes for the lung in neonatal C57BL/6 mice under consideration of biological, technical and experimental conditions. For that, we thoroughly selected candidates from commonly used reference genes side-by-side with novel ones by analyzing publicly available microarray datasets. We performed RT-qPCR of the selected candidate genes and analyzed their expression variability using GeNorm and Normfinder. Cell-specific expression of the candidate genes was analyzed using our own single-cell RNA-sequencing data from the developing mouse lung. Depending on the investigated conditions, i.e., developmental stages, sex, RNA quality, experimental condition (hyperoxia) and cell types, distinct candidate genes demonstrated stable expression confirming their eligibility as reliable reference genes. Our results provide valuable information for the selection of proper reference genes in studies investigating the neonatal mouse lung.
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Affiliation(s)
- H. Shin
- grid.4567.00000 0004 0483 2525Institute for Lung Biology and Disease and Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of German Center for Lung Research (DZL), Munich, Germany
| | - R. E. Morty
- grid.5253.10000 0001 0328 4908Department of Translational Pulmonology, University Hospital Heidelberg, Heidelberg, Germany ,Translational Lung Research Center, member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - J. M. Sucre
- grid.412807.80000 0004 1936 9916Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN USA
| | - N. M. Negretti
- grid.412807.80000 0004 1936 9916Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN USA
| | - M. Markmann
- grid.8664.c0000 0001 2165 8627Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Justus-Liebig-University, Giessen, Germany
| | - H. Hossain
- grid.440273.6Institute of Laboratory Medicine and Microbiology, Klinikum St. Marien Amberg and Kliniken Nordoberpfalz AG, Weiden, Germany
| | - S. Krauss-Etschmann
- grid.4567.00000 0004 0483 2525Institute for Lung Biology and Disease and Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of German Center for Lung Research (DZL), Munich, Germany ,grid.452624.3Present Address: Priority Area Chronic Lung Diseases, Early Life Origins of Chronic Lung Disease, Research Center Borstel, Leibniz Lung Center, German Center for Lung Research (DZL) and the Airway Research Center North (ARCN), Borstel, Germany ,grid.9764.c0000 0001 2153 9986Present Address: Institute for Experimental Medicine, Christian Albrechts University, German Center for Lung Research (DZL) and the Airway Research Center North (ARCN), Kiel, Germany
| | - S. Dehmel
- grid.4567.00000 0004 0483 2525Institute for Lung Biology and Disease and Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of German Center for Lung Research (DZL), Munich, Germany ,grid.4567.00000 0004 0483 2525Present Address: Strategy, Programs, Resources (SPR), Helmholtz Zentrum München, Munich, Germany
| | - A. Hilgendorff
- grid.4567.00000 0004 0483 2525Institute for Lung Biology and Disease and Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of German Center for Lung Research (DZL), Munich, Germany ,grid.5252.00000 0004 1936 973XCenter for Comprehensive Developmental Care (CDeCLMU), University Hospital, Ludwig-Maximilians-University, Munich, Germany
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