Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control

Show full item record



Permalink

http://hdl.handle.net/10138/163035

Citation

Katayama , S , Skoog , T , Jouhilahti , E-M , Siitonen , H A , Nuutila , K , Tervaniemi , M H , Vuola , J , Johnsson , A , Lonnerberg , P , Linnarsson , S , Elomaa , O , Kankuri , E & Kere , J 2015 , ' Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control ' , BMC Genomics , vol. 16 , 476 . https://doi.org/10.1186/s12864-015-1671-5

Title: Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control
Author: Katayama, Shintaro; Skoog, Tiina; Jouhilahti, Eeva-Mari; Siitonen, H. Annika; Nuutila, Kristo; Tervaniemi, Mari H.; Vuola, Jyrki; Johnsson, Anna; Lonnerberg, Peter; Linnarsson, Sten; Elomaa, Outi; Kankuri, Esko; Kere, Juha
Contributor: University of Helsinki, Karolinska Institutet
University of Helsinki, Research Programs Unit
University of Helsinki, Medicum
University of Helsinki, Research Programs Unit
University of Helsinki, Clinicum
University of Helsinki, Research Programs Unit
University of Helsinki, Medicum
University of Helsinki, Research Programs Unit
Date: 2015-06-25
Language: eng
Number of pages: 14
Belongs to series: BMC Genomics
ISSN: 1471-2164
URI: http://hdl.handle.net/10138/163035
Abstract: Background: Keratinocytes (KCs) are the most frequent cells in the epidermis, and they are often isolated and cultured in vitro to study the molecular biology of the skin. Cultured primary cells and various immortalized cells have been frequently used as skin models but their comparability to intact skin has been questioned. Moreover, when analyzing KC transcriptomes, fluctuation of polyA+ RNA content during the KCs' lifecycle has been omitted. Results: We performed STRT RNA sequencing on 10 ng samples of total RNA from three different sample types: i) epidermal tissue (split-thickness skin grafts), ii) cultured primary KCs, and iii) HaCaT cell line. We observed significant variation in cellular polyA+ RNA content between tissue and cell culture samples of KCs. The use of synthetic RNAs and SAMstrt in normalization enabled comparison of gene expression levels in the highly heterogenous samples and facilitated discovery of differences between the tissue samples and cultured cells. The transcriptome analysis sensitively revealed genes involved in KC differentiation in skin grafts and cell cycle regulation related genes in cultured KCs and emphasized the fluctuation of transcription factors and non-coding RNAs associated to sample types. Conclusions: The epidermal keratinocytes derived from tissue and cell culture samples showed highly different polyA+ RNA contents. The use of SAMstrt and synthetic RNA based normalization allowed the comparison between tissue and cell culture samples and thus proved to be valuable tools for RNA-seq analysis with translational approach. Transciptomics revealed clear difference both between tissue and cell culture samples and between primary KCs and immortalized HaCaT cells.
Subject: CELL-CYCLE PROGRESSION
EPIDERMAL-KERATINOCYTES
CANCER-CELLS
LINE
TRANSCRIPTOME
PROLIFERATION
SENESCENCE
MUTATIONS
MICRORNAS
PATHWAY
318 Medical biotechnology
3111 Biomedicine
1184 Genetics, developmental biology, physiology
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
art_3A10.1186_2Fs12864_015_1671_5.pdf 1.703Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record