Seon-Sook Han1, Woo Jin Kim1, Yoonki Hong1, Seok-Ho Hong1, Seung-Joon Lee1, Dong Ryeol Ryu1, Wonho Lee1, Yo Han Cho1, Seungkoo Lee2, Young-Joon Ryu3, Jun Yeon Won4, Hwanseok Rhee5, Jung Hoon Park5, Se Jin Jang6, Jae Seung Lee7, Chang-Min Choi8, Jae Cheol Lee9, Sang Do Lee7, Yeon-Mok Oh10. 1. Department of Internal Medicine, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea. 2. Department of Anatomic Pathology, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea. 3. Department of Pathology, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea. 4. Department of Otolaryngology, School of Medicine, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Kangwon-do 200-701, Republic of Korea. 5. Macrogen Bioinformatics Center, Macrogen, Seoul 153-781, Republic of Korea. 6. 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. 7. 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. 8. 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. 9. 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. 10. 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.
Abstract
INTRODUCTION: 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.
INTRODUCTION: 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: George S Krasnov; Alexey A Dmitriev; Nataliya V Melnikova; Andrew R Zaretsky; Tatiana V Nasedkina; Alexander S Zasedatelev; Vera N Senchenko; Anna V Kudryavtseva Journal: Nucleic Acids Res Date: 2016-01-14 Impact factor: 16.971
Authors: John A Haley; Elizabeth Haughney; Erica Ullman; James Bean; John D Haley; Marc Y Fink Journal: Front Oncol Date: 2014-12-08 Impact factor: 6.244
Authors: Gillian S Tomlinson; Niclas Thomas; Benjamin M Chain; Katharine Best; Nandi Simpson; Georgia Hardavella; James Brown; Angshu Bhowmik; Neal Navani; Samuel M Janes; Robert F Miller; Mahdad Noursadeghi Journal: Chest Date: 2016-01-12 Impact factor: 9.410