title: Whole Transcriptome Analysis of Pre-invasive and Invasive Early Squamous Lung Carcinoma in Archival Laser Microdissected Samples.
abstract: Preinvasive squamous cell cancer (PSCC) are local transformations of bronchial epithelia that are frequently observed in current or former smokers. Their different grades and sizes suggest a continuum of dysplastic change with increasing severity, which may culminate in invasive squamous cell carcinoma (ISCC). As a consequence of the difficulty in isolating cancerous cells from biopsies, the molecular pathology that underlies their histological variability remains largely unknown.
  
  
  
  To address this issue, we have employed microdissection to isolate normal bronchial epithelia and cancerous cells from low- and high-grade PSCC and ISCC, from paraffin embedded (FFPE) biopsies and determined gene expression using Affymetric Human Exon 1.0 ST arrays. Tests for differential gene expression were performed using the Bioconductor package limma followed by functional analyses of differentially expressed genes in IPA.
  
  
  
  Examination of differential gene expression showed small differences between low- and high-grade PSCC but substantial changes between PSCC and ISCC samples (184 vs 1200 p-value <0.05, fc ±1.75). However, the majority of the differentially expressed PSCC genes (142 genes: 77%) were shared with those in ISCC samples. Pathway analysis showed that these shared genes are associated with DNA damage response, DNA/RNA metabolism and inflammation as major biological themes. Cluster analysis identified 12 distinct patterns of gene expression including progressive up or down-regulation across PSCC and ISCC. Pathway analysis of incrementally up-regulated genes revealed again significant enrichment of terms related to DNA damage response, DNA/RNA metabolism, inflammation, survival and proliferation. Altered expression of selected genes was confirmed using RT-PCR, as well as immunohistochemistry in an independent set of 45 ISCCs.
  
  
  
  Gene expression profiles in PSCC and ISCC differ greatly in terms of numbers of genes with altered transcriptional activity. However, altered gene expression in PSCC affects canonical pathways and cellular and biological processes, such as inflammation and DNA damage response, which are highly consistent with hallmarks of cancer.
authors.affiliation: Qiagen GmbH, Hilden, 40724, Germany.
authors.forename: Andre
authors.initials: A
authors.lastname: Koper
authors.affiliation: Faculty of Life Science, University of Manchester, Manchester, England, M13 9PT, UK.
authors.forename: Leo A H
authors.initials: LA
authors.lastname: Zeef
authors.affiliation: Department of Pathology, University Hospital of South Manchester, Manchester, England, M23 9LT, UK.
authors.forename: Leena
authors.initials: L
authors.lastname: Joseph
authors.affiliation: Department of Pathology, University of Aberdeen, Aberdeen, Scotland, AB25 2ZD, UK.
authors.forename: Keith
authors.initials: K
authors.lastname: Kerr
authors.affiliation: Department of Pathology, Royal Liverpool University Hospital, Liverpool, England, L7 8XP, UK.
authors.forename: John
authors.initials: J
authors.lastname: Gosney
authors.affiliation: Department of Pharmacy and Pharmacology, University of Bath, Bath, England, BA 7AY, UK.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Lindsay
authors.affiliation: Manchester Thoracic Oncology Centre, University Hospital of South Manchester, Manchester, England, M23 9LT, UK. richard.booton@uhsm.nhs.uk.
authors.forename: Richard
authors.initials: R
authors.lastname: Booton
mesh_terms: D000368:Aged; D002294:Carcinoma, Squamous Cell / Q000378:metabolism* / Q000473:pathology*; D002478:Cells, Cultured; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D061346:Laser Capture Microdissection; D008175:Lung Neoplasms / Q000378:metabolism* / Q000473:pathology*; D008297:Male; D008875:Middle Aged; D009361:Neoplasm Invasiveness; D009363:Neoplasm Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D059467:Transcriptome; D014407:Tumor Cells, Cultured
chemical_list: D009363:Neoplasm Proteins; D014157:Transcription Factors
keywords: Exon arrays; Gene expression profiling; Invasive squamous cell cancer; Microdissection; Preinvasive squamous cell cancer