Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Oncology Letters
      • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Biomedical Reports
      • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • Information for Authors
    • Information for Reviewers
    • Information for Librarians
    • Information for Advertisers
    • Conferences
  • Language Editing
Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • For Authors
    • For Reviewers
    • For Librarians
    • For Advertisers
    • Conferences
  • Language Editing
Login Register Submit
  • This site uses cookies
  • You can change your cookie settings at any time by following the instructions in our Cookie Policy. To find out more, you may read our Privacy Policy.

    I agree
Search articles by DOI, keyword, author or affiliation
Search
Advanced Search
presentation
Oncology Letters
Join Editorial Board Propose a Special Issue
Print ISSN: 1792-1074 Online ISSN: 1792-1082
Journal Cover
August-2017 Volume 14 Issue 2

Full Size Image

Sign up for eToc alerts
Recommend to Library

Journals

International Journal of Molecular Medicine

International Journal of Molecular Medicine

International Journal of Molecular Medicine is an international journal devoted to molecular mechanisms of human disease.

International Journal of Oncology

International Journal of Oncology

International Journal of Oncology is an international journal devoted to oncology research and cancer treatment.

Molecular Medicine Reports

Molecular Medicine Reports

Covers molecular medicine topics such as pharmacology, pathology, genetics, neuroscience, infectious diseases, molecular cardiology, and molecular surgery.

Oncology Reports

Oncology Reports

Oncology Reports is an international journal devoted to fundamental and applied research in Oncology.

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine is an international journal devoted to laboratory and clinical medicine.

Oncology Letters

Oncology Letters

Oncology Letters is an international journal devoted to Experimental and Clinical Oncology.

Biomedical Reports

Biomedical Reports

Explores a wide range of biological and medical fields, including pharmacology, genetics, microbiology, neuroscience, and molecular cardiology.

Molecular and Clinical Oncology

Molecular and Clinical Oncology

International journal addressing all aspects of oncology research, from tumorigenesis and oncogenes to chemotherapy and metastasis.

World Academy of Sciences Journal

World Academy of Sciences Journal

Multidisciplinary open-access journal spanning biochemistry, genetics, neuroscience, environmental health, and synthetic biology.

International Journal of Functional Nutrition

International Journal of Functional Nutrition

Open-access journal combining biochemistry, pharmacology, immunology, and genetics to advance health through functional nutrition.

International Journal of Epigenetics

International Journal of Epigenetics

Publishes open-access research on using epigenetics to advance understanding and treatment of human disease.

Medicine International

Medicine International

An International Open Access Journal Devoted to General Medicine.

Journal Cover
August-2017 Volume 14 Issue 2

Full Size Image

Sign up for eToc alerts
Recommend to Library

  • Article
  • Citations
    • Cite This Article
    • Download Citation
    • Create Citation Alert
    • Remove Citation Alert
    • Cited By
  • Similar Articles
    • Related Articles (in Spandidos Publications)
    • Similar Articles (Google Scholar)
    • Similar Articles (PubMed)
  • Download PDF
  • Download XML
  • View XML
Article Open Access

Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing

  • Authors:
    • Zulei Li
    • Kai Zhao
    • Hui Tian
  • View Affiliations / Copyright

    Affiliations: Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China, Department of Thoracic Surgery, Zibo Central Hospital, Zibo, Shandong 255036, P.R. China
    Copyright: © Li et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 1519-1525
    |
    Published online on: June 2, 2017
       https://doi.org/10.3892/ol.2017.6300
  • Expand metrics +
Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )
Cited By (CrossRef): 0 citations Loading Articles...

This article is mentioned in:



Abstract

Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, with high morbidity and mortality rates. Numerous diagnosis and treatment methods have been proposed, and the prognosis of NSCLC has improved to a certain extent. However, the mechanisms of NSCLC remain largely unknown, and additional studies are required. In the present study, the RNA sequencing dataset of NSCLC was downloaded from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/). The clean reads obtained from the raw data were mapped to the University of California Santa Cruz human genome (hg19), based on TopHat, and were assembled into transcripts via Cufflink. The differential expression (DE) and differential alternative splicing (DAS) genes were screened out through Cuffdiff and rMATS, respectively. The significantly enriched gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes pathways were obtained through the Database of Annotation, Visualization and Integrated Discovery (DAVID). Different numbers of DE and DAS genes were identified in different types of NSCLC samples, but a number of common functions and pathways were obtained, including biological processes associated with abnormal immune and cell activity. GO terms and pathways associated with substance metabolism, including the insulin signaling pathway and oxidative phosphorylation, were enriched in DAS genes rather than DE genes. Integrated analysis of differential expression and alternative splicing may be helpful in understanding the mechanisms of NSCLC, in addition to its early diagnosis and treatment.
View Figures

Figure 1

Figure 2

Figure 3

Figure 4

View References

1 

He X, Wang J and Li Y: Efficacy and safety of docetaxel for advanced non-small-cell lung cancer: A meta-analysis of Phase III randomized controlled trials. Onco Targets Ther. 8:2023–2031. 2015. View Article : Google Scholar : PubMed/NCBI

2 

She J, Yang P, Hong Q and Bai C: Lung cancer in China: Challenges and interventions. Chest. 143:1117–1126. 2013. View Article : Google Scholar : PubMed/NCBI

3 

Santarpia M, González-Cao M, Viteri S, Karachaliou N, Altavilla G and Rosell R: Programmed cell death protein-1/programmed cell death ligand-1 pathway inhibition and predictive biomarkers: Understanding transforming growth factor-beta role. Transl Lung Cancer Res. 4:728–742. 2015.PubMed/NCBI

4 

Nakajima Y, Akiyama H, Kinoshita H, Atari M, Fukuhara M, Saito Y, Sakai H and Uramoto H: Case report of two patients having successful surgery for lung cancer after treatment for Grade 2 radiation pneumonitis. Ann Med Surg (Lond). 5:1–4. 2015. View Article : Google Scholar : PubMed/NCBI

5 

Wieder T, Brenner E, Braumüller H and Röcken M: Immunotherapy of melanoma: Efficacy and mode of action. J Dtsch Dermatol Ges. 14:28–37. 2016. View Article : Google Scholar : PubMed/NCBI

6 

Pilotto S, Molina-Vila MA, Karachaliou N, Carbognin L, Viteri S, González-Cao M, Bria E, Tortora G and Rosell R: Integrating the molecular background of targeted therapy and immunotherapy in lung cancer: A way to explore the impact of mutational landscape on tumor immunogenicity. Transl Lung Cancer Res. 4:721–727. 2015.PubMed/NCBI

7 

Kobold S, Duewell P, Schnurr M, Subklewe M, Rothenfusser S and Endres S: Immunotherapy in tumors. Dtsch Arztebl Int. 112:809–815. 2015.PubMed/NCBI

8 

Morozova O and Marra MA: Applications of next-generation sequencing technologies in functional genomics. Genomics. 92:255–264. 2008. View Article : Google Scholar : PubMed/NCBI

9 

Riccardo F, Arigoni M, Buson G, Zago E, Iezzi M, Longo D, Carrara M, Fiore A, Nuzzo S, Bicciato S, et al: Characterization of a genetic mouse model of lung cancer: A promise to identify non-small cell lung cancer therapeutic targets and biomarkers. BMC Genomics. 15 Suppl 3:12014. View Article : Google Scholar : PubMed/NCBI

10 

Han SS, Kim WJ, Hong Y, Hong SH, Lee SJ, Ryu DR, Lee W, Cho YH, Lee S, Ryu YJ, et al: RNA sequencing identifies novel markers of non-small cell lung cancer. Lung Cancer. 84:229–235. 2014. View Article : Google Scholar : PubMed/NCBI

11 

Bisognin A, Pizzini S, Perilli L, Esposito G, Mocellin S, Nitti D, Zanovello P, Bortoluzzi S and Mandruzzato S: An integrative framework identifies alternative splicing events in colorectal cancer development. Mol Oncol. 8:129–141. 2014. View Article : Google Scholar : PubMed/NCBI

12 

Durrans A, Gao D, Gupta R, Fischer KR, Choi H, El Rayes T, Ryu S, Nasar A, Spinelli CF, Andrews W, et al: Identification of reprogrammed myeloid cell transcriptomes in NSCLC. PLoS One. 10:e01291232015. View Article : Google Scholar : PubMed/NCBI

13 

Andrews S: FastQC: A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/January 10–2016

14 

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL and Pachter L: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 7:562–578. 2012. View Article : Google Scholar : PubMed/NCBI

15 

Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q and Xing Y: rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci USA. 111:pp. E5593–E5601. 2014; View Article : Google Scholar : PubMed/NCBI

16 

da W Huang, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57. 2009.PubMed/NCBI

17 

Sang Y, Bi X, Liu Y, Zhang W and Wang D: Adverse prognostic impact of TGFB1 T869C polymorphism in non-small-cell lung cancer. Onco Targets Ther. 10:1513–1518. 2017. View Article : Google Scholar : PubMed/NCBI

18 

Han Y, Gao S, Muegge K, Zhang W and Zhou B: Advanced applications of RNA sequencing and challenges. Bioinform Biol Insights. 9 Suppl 1:29–46. 2015. View Article : Google Scholar : PubMed/NCBI

19 

Krishnaswamy S, Mohammed AK, Amer OE, Tripathi G, Alokail MS and Al-Daghri NM: Novel splicing variants of recepteur d'origine nantais (RON) tyrosine kinase involving exons 15–19 in lung cancer. Lung Cancer. 92:41–46. 2016. View Article : Google Scholar : PubMed/NCBI

20 

Fan YC, Min L, Chen H and Liu YL: Alternative splicing isoform of T cell factor 4K suppresses the proliferation and metastasis of non-small cell lung cancer cells. Genet Mol Res. 14:14009–14018. 2015. View Article : Google Scholar : PubMed/NCBI

21 

Wang X, Xu X, Lu X, Zhang Y and Pan W: Transcriptome Bioinformatical analysis of vertebrate stages of Schistosoma japonicum reveals alternative splicing events. PLoS One. 10:e01384702015. View Article : Google Scholar : PubMed/NCBI

22 

Hide WA, Babenko VN, van Heusden PA, Seoighe C and Kelso JF: The contribution of exon-skipping events on chromosome 22 to protein coding diversity. Genome Res. 11:1848–1853. 2001.PubMed/NCBI

23 

Scagliotti GV and Novello S: The role of the insulin-like growth factor signaling pathway in non-small cell lung cancer and other solid tumors. Cancer Treat Rev. 38:292–302. 2012. View Article : Google Scholar : PubMed/NCBI

24 

Sun Y, Zheng S, Torossian A, Speirs CK, Schleicher S, Giacalone NJ, Carbone DP, Zhao Z and Lu B: Role of insulin-like growth factor-1 signaling pathway in cisplatin-resistant lung cancer cells. Int J Radiat Oncol Biol Phys. 82:e563–e572. 2012. View Article : Google Scholar : PubMed/NCBI

25 

Dávila D, Fernández S and Torres-Alemán I: Astrocyte resilience to oxidative stress induced by insulin-like growth factor I (IGF-I) involves preserved AKT (protein kinase B) activity. J Biol Chem. 291:2510–2523. 2016. View Article : Google Scholar : PubMed/NCBI

26 

Khawaja T, Chokshi A, Ji R, Kato TS, Xu K, Zizola C, Wu C, Forman DE, Ota T, Kennel P, et al: Ventricular assist device implantation improves skeletal muscle function, oxidative capacity, and growth hormone/insulin-like growth factor-1 axis signaling in patients with advanced heart failure. J Cachexia Sarcopenia Muscle. 5:297–305. 2014. View Article : Google Scholar : PubMed/NCBI

27 

De Palma M: The role of the immune system in cancer: From mechanisms to clinical applications. Biochim Biophys Acta. 1865:1–2. 2016.PubMed/NCBI

28 

Soto-Ortiz L and Finley SD: A cancer treatment based on synergy between anti-angiogenic and immune cell therapies. J Theor Biol. 394:197–211. 2016. View Article : Google Scholar : PubMed/NCBI

29 

Boros LG, D'Agostino DP, Katz HE, Roth JP, Meuillet EJ and Somlyai G: Submolecular regulation of cell transformation by deuterium depleting water exchange reactions in the tricarboxylic acid substrate cycle. Med Hypotheses. 87:69–74. 2016. View Article : Google Scholar : PubMed/NCBI

30 

Oosterveld LP, Allen JC Jr, Ng EY, Seah SH, Tay KY, Au WL, Tan EK and Tan LC: Greater motor progression in patients with Parkinson disease who carry LRRK2 risk variants. Neurology. 85:1039–1042. 2015. View Article : Google Scholar : PubMed/NCBI

31 

Marder K, Wang Y, Alcalay RN, Mejia-Santana H, Tang MX, Lee A, Raymond D, Mirelman A, Saunders-Pullman R, Clark L, et al: Age-specific penetrance of LRRK2 G2019S in the Michael J. Fox Ashkenazi Jewish LRRK2 consortium. Neurology. 85:89–95. 2015. View Article : Google Scholar : PubMed/NCBI

32 

Lee JW and Cannon JR: LRRK2 mutations and neurotoxicant susceptibility. Exp Biol Med (Maywood). 240:752–759. 2015. View Article : Google Scholar : PubMed/NCBI

33 

Bae JR and Lee BD: Function and dysfunction of leucine-rich repeat kinase 2 (LRRK2): Parkinson's disease and beyond. BMB Reports. 48:243–248. 2015. View Article : Google Scholar : PubMed/NCBI

34 

Looyenga BD, Furge KA, Dykema KJ, Koeman J, Swiatek PJ, Giordano TJ, West AB, Resau JH, Teh BT and MacKeigan JP: Chromosomal amplification of leucine-rich repeat kinase-2 (LRRK2) is required for oncogenic MET signaling in papillary renal and thyroid carcinomas. Proc Natl Acad Sci USA. 108:pp. 1439–1444. 2011; View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Li Z, Zhao K and Tian H: Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing. Oncol Lett 14: 1519-1525, 2017.
APA
Li, Z., Zhao, K., & Tian, H. (2017). Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing. Oncology Letters, 14, 1519-1525. https://doi.org/10.3892/ol.2017.6300
MLA
Li, Z., Zhao, K., Tian, H."Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing". Oncology Letters 14.2 (2017): 1519-1525.
Chicago
Li, Z., Zhao, K., Tian, H."Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing". Oncology Letters 14, no. 2 (2017): 1519-1525. https://doi.org/10.3892/ol.2017.6300
Copy and paste a formatted citation
x
Spandidos Publications style
Li Z, Zhao K and Tian H: Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing. Oncol Lett 14: 1519-1525, 2017.
APA
Li, Z., Zhao, K., & Tian, H. (2017). Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing. Oncology Letters, 14, 1519-1525. https://doi.org/10.3892/ol.2017.6300
MLA
Li, Z., Zhao, K., Tian, H."Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing". Oncology Letters 14.2 (2017): 1519-1525.
Chicago
Li, Z., Zhao, K., Tian, H."Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing". Oncology Letters 14, no. 2 (2017): 1519-1525. https://doi.org/10.3892/ol.2017.6300
Follow us
  • Twitter
  • LinkedIn
  • Facebook
About
  • Spandidos Publications
  • Careers
  • Cookie Policy
  • Privacy Policy
How can we help?
  • Help
  • Live Chat
  • Contact
  • Email to our Support Team