title: Characterization of gene expression profiles for different types of mast cells pooled from mouse stomach subregions by an RNA amplification method.
abstract: BACKGROUND
  Mast cells (MCs) play pivotal roles in allergy and innate immunity and consist of heterogenous subclasses. However, the molecular basis determining the different characteristics of these multiple MC subclasses remains unclear.
  
  
  RESULTS
  To approach this, we developed a method of RNA extraction/amplification for intact in vivo MCs pooled from frozen tissue sections, which enabled us to obtain the global gene expression pattern of pooled MCs belonging to the same subclass. MCs were isolated from the submucosa (sMCs) and mucosa (mMCs) of mouse stomach sections, respectively, 15 cells were pooled, and their RNA was extracted, amplified and subjected to microarray analysis. Known marker genes specific for mMCs and sMCs showed expected expression trends, indicating accuracy of the analysis. We identified 1,272 genes showing significantly different expression levels between sMCs and mMCs, and classified them into clusters on the basis of similarity of their expression profiles compared with bone marrow-derived MCs, which are the cultured MCs with so-called 'immature' properties. Among them, we found that several key genes such as Notch4 had sMC-biased expression and Ptgr1 had mMC-biased expression. Furthermore, there is a difference in the expression of several genes including extracellular matrix protein components, adhesion molecules, and cytoskeletal proteins between the two MC subclasses, which may reflect functional adaptation of each MC to the mucosal or submucosal environment in the stomach.
  
  
  CONCLUSIONS
  By using the method of RNA amplification from pooled intact MCs, we characterized the distinct gene expression profiles of sMCs and mMCs in the mouse stomach. Our findings offer insight into possible unidentified properties specific for each MC subclass.
authors.affiliation: Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan. Soken.Tsuchiya@f13.mbox.media.kyoto-u.ac.jp
authors.forename: Soken
authors.initials: S
authors.lastname: Tsuchiya
authors.forename: Yuki
authors.initials: Y
authors.lastname: Tachida
authors.forename: Eri
authors.initials: E
authors.lastname: Segi-Nishida
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Okuno
authors.forename: Shigero
authors.initials: S
authors.lastname: Tamba
authors.forename: Gozoh
authors.initials: G
authors.lastname: Tsujimoto
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tanaka
authors.forename: Yukihiko
authors.initials: Y
authors.lastname: Sugimoto
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D005753:Gastric Mucosa / Q000166:cytology / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D008407:Mast Cells / Q000378:metabolism*; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods
chemical_list: D012313:RNA