title: RNA sequencing of sessile serrated colon polyps identifies differentially expressed genes and immunohistochemical markers.
abstract: BACKGROUND
  Sessile serrated adenomas/polyps (SSA/Ps) may account for 20-30% of colon cancers. Although large SSA/Ps are generally recognized phenotypically, small (<1 cm) or dysplastic SSA/Ps are difficult to differentiate from hyperplastic or small adenomatous polyps by endoscopy and histopathology. Our aim was to define the comprehensive gene expression phenotype of SSA/Ps to better define this cancer precursor.
  
  
  RESULTS
  RNA sequencing was performed on 5' capped RNA from seven SSA/Ps collected from patients with the serrated polyposis syndrome (SPS) versus eight controls. Highly expressed genes were analyzed by qPCR in additional SSA/Ps, adenomas and controls. The cellular localization and level of gene products were examined by immunohistochemistry in syndromic and sporadic SSA/Ps, adenomatous and hyperplastic polyps and controls. We identified 1,294 differentially expressed annotated genes, with 106 increased ≥10-fold, in SSA/Ps compared to controls. Comparing these genes with an array dataset for adenomatous polyps identified 30 protein coding genes uniquely expressed ≥10-fold in SSA/Ps. Biological pathways altered in SSA/Ps included mucosal integrity, cell adhesion, and cell development. Marked increased expression of MUC17, the cell junction protein genes VSIG1 and GJB5, and the antiapoptotic gene REG4 were found in SSA/Ps, relative to controls and adenomas, were verified by qPCR analysis of additional SSA/Ps (n = 21) and adenomas (n = 10). Immunohistochemical staining of syndromic (n≥11) and sporadic SSA/Ps (n≥17), adenomatous (n≥13) and hyperplastic (n≥10) polyps plus controls (n≥16) identified unique expression patterns for VSIG1 and MUC17 in SSA/Ps.
  
  
  CONCLUSIONS
  A subset of genes and pathways are uniquely increased in SSA/Ps, compared to adenomatous polyps, thus supporting the concept that cancer develops by different pathways in these phenotypically distinct polyps with markedly different gene expression profiles. Immunostaining for a subset of these genes differentiates both syndromic and sporadic SSA/Ps from adenomatous and hyperplastic polyps.
authors.affiliation: Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: Don A
authors.initials: DA
authors.lastname: Delker
authors.affiliation: Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: Brett M
authors.initials: BM
authors.lastname: McGettigan
authors.affiliation: Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: Priyanka
authors.initials: P
authors.lastname: Kanth
authors.affiliation: Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: Stelian
authors.initials: S
authors.lastname: Pop
authors.affiliation: Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: Deborah W
authors.initials: DW
authors.lastname: Neklason
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America ; Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: Mary P
authors.initials: MP
authors.lastname: Bronner
authors.affiliation: Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America ; Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: Randall W
authors.initials: RW
authors.lastname: Burt
authors.affiliation: Department of Medicine, University of Utah, Salt Lake City, Utah, United States of America ; Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America ; Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America ; University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America ; The Central Arkansas Veterans Healthcare System, Little Rock, Arkansas, United States of America.
authors.forename: Curt H
authors.initials: CH
authors.lastname: Hagedorn
mesh_terms: D000236:Adenoma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology*; D000368:Aged; D000951:Antigens, Neoplasm / Q000378:metabolism; D016000:Cluster Analysis; D003106:Colon / Q000378:metabolism; D003110:Colonic Neoplasms / Q000235:genetics / Q000378:metabolism; D003111:Colonic Polyps / Q000235:genetics* / Q000473:pathology*; D003113:Colonoscopy; D017630:Connexins / Q000378:metabolism; D004252:DNA Mutational Analysis; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D007150:Immunohistochemistry; D037181:Lectins, C-Type / Q000378:metabolism; D008297:Male; D008562:Membrane Glycoproteins / Q000378:metabolism; D008875:Middle Aged; D009077:Mucins / Q000378:metabolism; D000073718:Pancreatitis-Associated Proteins; D016133:Polymerase Chain Reaction; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D000951:Antigens, Neoplasm; D017630:Connexins; C000594152:GJB5 protein, human; D037181:Lectins, C-Type; C450720:MUC17 protein, human; D008562:Membrane Glycoproteins; D009077:Mucins; D000073718:Pancreatitis-Associated Proteins; C428528:REG4 protein, human; C510166:VSIG1 protein, human; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf