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Stegmayr J, Alsafadi HN, Langwiński W, Niroomand A, Lindstedt S, Leigh ND, Wagner DE. Isolation of high-yield and -quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts. Am J Physiol Lung Cell Mol Physiol 2020; 320:L232-L240. [PMID: 33112185 DOI: 10.1152/ajplung.00401.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Precision-cut lung slices (PCLS) have gained increasing interest as a model to study lung biology/disease and screening novel therapeutics. In particular, PCLS derived from human tissue can better recapitulate some aspects of lung biology/disease as compared with animal models. Several experimental readouts have been established for use with PCLS, but obtaining high-yield and -quality RNA for downstream analysis has remained challenging. This is particularly problematic for utilizing the power of next-generation sequencing techniques, such as RNA-sequencing (RNA-seq), for nonbiased and high-throughput analysis of PCLS human cohorts. In the current study, we present a novel approach for isolating high-quality RNA from a small amount of tissue, including diseased human tissue, such as idiopathic pulmonary fibrosis. We show that the RNA isolated using this method has sufficient quality for RT-qPCR and RNA-seq analysis. Furthermore, the RNA-seq data from human PCLS could be used in several established computational pipelines, including deconvolution of bulk RNA-seq data using publicly available single-cell RNA-seq data. Deconvolution using Bisque revealed a diversity of cell populations in human PCLS, including several immune cell populations, which correlated with cell populations known to be present and aberrant in human disease.
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Affiliation(s)
- John Stegmayr
- Department of Experimental Medical Sciences, Lund University, Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Hani N Alsafadi
- Department of Experimental Medical Sciences, Lund University, Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Wojciech Langwiński
- Department of Experimental Medical Sciences, Lund University, Lund, Sweden.,Department of Pediatric Pulmonology, Allergy, and Clinical Immunology, Poznan University of Medical Science, Poznan, Poland
| | - Anna Niroomand
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Department of Thoracic Surgery, Lund University, Lund, Sweden
| | - Sandra Lindstedt
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Department of Thoracic Surgery, Lund University, Lund, Sweden
| | - Nicholas D Leigh
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.,Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Darcy E Wagner
- Department of Experimental Medical Sciences, Lund University, Lund, Sweden.,Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.,Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
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