title: RNA sequencing identifies novel markers of non-small cell lung cancer.
abstract: BACKGROUND
  The development of reliable gene expression profiling technology increasingly impacts our understanding of lung cancer biology. Here, we used RNA sequencing (RNA-Seq) to compare the transcriptomes of non-small cell lung cancer (NSCLC) and normal lung tissues and to investigate expression in lung cancer tissues.
  
  
  METHODS
  We enrolled 88 male patients (mean age, 61.2 years) with NSCLC. RNA-Seq was performed on 88 pairs of NSCLC tumor tissue and non-tumor tissue from 54 patients with adenocarcinoma and 34 patients with squamous cell carcinoma. Immunohistochemistry was performed to validate differential candidate gene expression in a different NSCLC group.
  
  
  RESULTS
  RNA-Seq produced 25.41 × 10(6) (± 8.90 × 10(6)) reads in NSCLC tissues and 24.70×10(6) (± 4.70 × 10(6)) reads in normal lung tissues [mean (± standard deviation)]. Among the genes expressed in both tissues, 335 were upregulated and 728 were downregulated ≥ 2-fold (p < 0.001). Four upregulated genes - CBX3, GJB2, CRABP2, and DSP - not previously reported in lung cancer were studied further. Their altered expression was verified by immunohistochemistry in a different set of NSCLC tissues (n = 154). CBX3 was positive in 90.3% (139 cases) of the samples; GJB2, in 22.7% (35 cases); CRABP2, in 72.1% (111 cases); and DSP, in 17.5% (27 cases). The positive rate of CRABP2 was higher in adenocarcinoma than squamous cell carcinoma (p < 0.01).
  
  
  CONCLUSIONS
  CBX3 and CRABP2 expression was markedly increased in lung cancer tissues and especially CRABP2 may be promising candidate genes in lung adenocarcinoma.
authors.affiliation: Department of Internal Medicine, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Seon-Sook
authors.initials: SS
authors.lastname: Han
authors.affiliation: Department of Internal Medicine, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Woo Jin
authors.initials: WJ
authors.lastname: Kim
authors.affiliation: Department of Internal Medicine, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Yoonki
authors.initials: Y
authors.lastname: Hong
authors.affiliation: Department of Internal Medicine, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Seok-Ho
authors.initials: SH
authors.lastname: Hong
authors.affiliation: Department of Internal Medicine, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Seung-Joon
authors.initials: SJ
authors.lastname: Lee
authors.affiliation: Department of Internal Medicine, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Dong Ryeol
authors.initials: DR
authors.lastname: Ryu
authors.affiliation: Department of Internal Medicine, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Wonho
authors.initials: W
authors.lastname: Lee
authors.affiliation: Department of Internal Medicine, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Yo Han
authors.initials: YH
authors.lastname: Cho
authors.affiliation: Department of Anatomic Pathology, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Seungkoo
authors.initials: S
authors.lastname: Lee
authors.affiliation: Department of Pathology, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Young-Joon
authors.initials: YJ
authors.lastname: Ryu
authors.affiliation: Department of Otolaryngology, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea.
authors.forename: Jun Yeon
authors.initials: JY
authors.lastname: Won
authors.affiliation: Macrogen Bioinformatics Center, Macrogen, Seoul 153-781, Republic of Korea.
authors.forename: Hwanseok
authors.initials: H
authors.lastname: Rhee
authors.affiliation: Macrogen Bioinformatics Center, Macrogen, Seoul 153-781, Republic of Korea.
authors.forename: Jung Hoon
authors.initials: JH
authors.lastname: Park
authors.affiliation: Department of Pathology and Asan Center for Cancer Genome Discovery, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea.
authors.forename: Se Jin
authors.initials: SJ
authors.lastname: Jang
authors.affiliation: Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea; Clinical Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea.
authors.forename: Jae Seung
authors.initials: JS
authors.lastname: Lee
authors.affiliation: Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea.
authors.forename: Chang-Min
authors.initials: CM
authors.lastname: Choi
authors.affiliation: Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea.
authors.forename: Jae Cheol
authors.initials: JC
authors.lastname: Lee
authors.affiliation: Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea; Clinical Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea.
authors.forename: Sang Do
authors.initials: SD
authors.lastname: Lee
authors.affiliation: Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea; Clinical Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea. Electronic address: ymoh55@amc.seoul.kr.
authors.forename: Yeon-Mok
authors.initials: YM
authors.lastname: Oh
mesh_terms: D000368:Aged; D014408:Biomarkers, Tumor / Q000032:analysis* / Q000235:genetics; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics*; D002868:Chromosomal Proteins, Non-Histone / Q000096:biosynthesis* / Q000235:genetics; D000072259:Connexin 26; D017630:Connexins; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007150:Immunohistochemistry; D008175:Lung Neoplasms / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D060888:Real-Time Polymerase Chain Reaction; D018168:Receptors, Retinoic Acid / Q000096:biosynthesis* / Q000235:genetics; D017423:Sequence Analysis, RNA; D046888:Tissue Array Analysis; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D014408:Biomarkers, Tumor; C518294:CBX3 protein, human; D002868:Chromosomal Proteins, Non-Histone; D017630:Connexins; C000607042:GJB2 protein, human; D018168:Receptors, Retinoic Acid; C082928:retinoic acid binding protein II, cellular; D000072259:Connexin 26
keywords: Carcinoma, Non-small cell lung; Gene expression profiling; Sequence analysis, RNA; Transcriptome