PMID- 33112185
OWN - NLM
STAT- MEDLINE
DCOM- 20210323
LR  - 20210323
IS  - 1522-1504 (Electronic)
IS  - 1040-0605 (Linking)
VI  - 320
IP  - 2
DP  - 2021 Feb 1
TI  - Isolation of high-yield and -quality RNA from human precision-cut lung slices for 
      RNA-sequencing and computational integration with larger patient cohorts.
PG  - L232-L240
LID - 10.1152/ajplung.00401.2020 [doi]
AB  - 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.
FAU - Stegmayr, John
AU  - Stegmayr J
AUID- ORCID: 0000-0002-8167-9259
AD  - Department of Experimental Medical Sciences, Lund University, Lund, Sweden.
AD  - Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
AD  - Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
FAU - Alsafadi, Hani N
AU  - Alsafadi HN
AUID- ORCID: 0000-0002-1186-2517
AD  - Department of Experimental Medical Sciences, Lund University, Lund, Sweden.
AD  - Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
AD  - Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
FAU - Langwinski, Wojciech
AU  - Langwinski W
AD  - Department of Experimental Medical Sciences, Lund University, Lund, Sweden.
AD  - Department of Pediatric Pulmonology, Allergy, and Clinical Immunology, Poznan 
      University of Medical Science, Poznan, Poland.
FAU - Niroomand, Anna
AU  - Niroomand A
AD  - Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
AD  - Department of Thoracic Surgery, Lund University, Lund, Sweden.
FAU - Lindstedt, Sandra
AU  - Lindstedt S
AUID- ORCID: 0000-0003-4484-6473
AD  - Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
AD  - Department of Thoracic Surgery, Lund University, Lund, Sweden.
FAU - Leigh, Nicholas D
AU  - Leigh ND
AUID- ORCID: 0000-0002-6978-6254
AD  - Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
AD  - Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
AD  - Department of Laboratory Medicine, Lund University, Lund, Sweden.
FAU - Wagner, Darcy E
AU  - Wagner DE
AUID- ORCID: 0000-0003-3794-1309
AD  - Department of Experimental Medical Sciences, Lund University, Lund, Sweden.
AD  - Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
AD  - Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20201028
PL  - United States
TA  - Am J Physiol Lung Cell Mol Physiol
JT  - American journal of physiology. Lung cellular and molecular physiology
JID - 100901229
RN  - 63231-63-0 (RNA)
SB  - IM
MH  - Animals
MH  - Female
MH  - Humans
MH  - *Idiopathic Pulmonary Fibrosis/genetics/metabolism
MH  - *Lung/chemistry/metabolism
MH  - Male
MH  - Mice
MH  - *Microdissection
MH  - Middle Aged
MH  - *RNA/chemistry/genetics/isolation & purification/metabolism
MH  - *RNA-Seq
OTO - NOTNLM
OT  - Bisque
OT  - RNA isolation
OT  - RNA-sequencing
OT  - deconvolution
OT  - precision-cut lung slices
EDAT- 2020/10/29 06:00
MHDA- 2021/03/24 06:00
CRDT- 2020/10/28 12:10
PHST- 2020/10/29 06:00 [pubmed]
PHST- 2021/03/24 06:00 [medline]
PHST- 2020/10/28 12:10 [entrez]
AID - 10.1152/ajplung.00401.2020 [doi]
PST - ppublish
SO  - Am J Physiol Lung Cell Mol Physiol. 2021 Feb 1;320(2):L232-L240. doi: 
      10.1152/ajplung.00401.2020. Epub 2020 Oct 28.