title: Differential Gene Expression Landscape of Co-Existing Cervical Pre-Cancer Lesions Using RNA-seq.
abstract: Genetic changes occurring in different stages of pre-cancer lesions reflect causal events initiating and promoting the progression to cancer. Co-existing pre-cancerous lesions including low- and high-grade squamous intraepithelial lesion (LGSIL and HGSIL), and adjacent "normal" cervical epithelium from six formalin-fixed paraffin-embedded samples were selected. Tissues from these 18 samples were isolated using laser-capture microdissection, RNA was extracted and sequenced. RNA-sequencing generated 2.4 billion raw reads in 18 samples, of which ~50.1% mapped to known and annotated genes in the human genome. There were 40 genes up-regulated and 3 down-regulated (normal to LGSIL) in at least one-third of the sample pairs (same direction and FDR p < 0.05) including S100A7 and KLK6. Previous studies have shown that S110A7 and KLK7 are up-regulated in several other cancers, whereas CCL18, CFTR, and SLC6A14, also differentially expressed in two samples, are up-regulated specifically in cervical cancer. These differentially expressed genes in normal to LGSIL progression were enriched in pathways related to epithelial cell differentiation, keratinocyte differentiation, peptidase, and extracellular activities. In progression from LGSIL to HGSIL, two genes were up-regulated and five down-regulated in at least two samples. Further investigations using co-existing samples, which account for all internal confounders, will provide insights to better understand progression of cervical pre-cancer.
authors.affiliation: Department of Epidemiology, University of Alabama at Birmingham , Birmingham, AL , USA.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Royse
authors.affiliation: Department of Biostatistics, University of Alabama at Birmingham , Birmingham, AL , USA.
authors.forename: Degui
authors.initials: D
authors.lastname: Zhi
authors.affiliation: Department of Pathology, University of Alabama at Birmingham , Birmingham, AL , USA.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Conner
authors.affiliation: Cellular and Molecular Neuropathology Core, University of Alabama at Birmingham , Birmingham, AL , USA.
authors.forename: Buffie
authors.initials: B
authors.lastname: Clodfelder-Miller
authors.affiliation: Department of Biostatistics, University of Alabama at Birmingham , Birmingham, AL , USA.
authors.forename: Vinodh
authors.initials: V
authors.lastname: Srinivasasainagendra
authors.affiliation: Department of Biostatistics, University of Alabama at Birmingham , Birmingham, AL , USA.
authors.forename: Laura Kelly
authors.initials: LK
authors.lastname: Vaughan
authors.affiliation: Department of Epidemiology, University of Alabama at Birmingham , Birmingham, AL , USA.
authors.forename: Christine F
authors.initials: CF
authors.lastname: Skibola
authors.affiliation: Department of Genetics, University of Alabama at Birmingham , Birmingham, AL , USA.
authors.forename: David K
authors.initials: DK
authors.lastname: Crossman
authors.affiliation: Hudson Alpha Institute for Biotechnology , Huntsville, AL , USA.
authors.forename: Shawn
authors.initials: S
authors.lastname: Levy
authors.affiliation: Department of Epidemiology, University of Alabama at Birmingham , Birmingham, AL , USA.
authors.forename: Sadeep
authors.initials: S
authors.lastname: Shrestha
keywords: RNA-sequencing; cervical dysplasia; co-existing lesions; gene expression; human genome