Transcriptional profiling of endobronchial ultrasound-guided lymph node samples aids diagnosis of mediastinal lymphadenopathy

Chest

Volumn 149, Issue 2, 2016, Pages 535-544

  Tomlinson, Gillian S ^a   Thomas, Niclas ^a   Chain, Benjamin M ^a   Best, Katharine ^a   Simpson, Nandi ^a   Hardavella, Georgia ^a   Brown, James ^a   Bhowmik, Angshu ^b   Navani, Neal ^a,c   Janes, Samuel M ^a   Miller, Robert F ^a   Noursadeghi, Mahdad ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b HOMERTON UNIVERSITY HOSPITAL   (United Kingdom)

^c UNIVERSITY COLLEGE LONDON HOSPITALS   (United Kingdom)

Author keywords

Cancer; Machine learning; Sarcoidosis; Transcriptome; Tuberculosis

Indexed keywords

ADULT; AGED; ARTICLE; DIAGNOSTIC TEST ACCURACY STUDY; DISEASE CLASSIFICATION; ENDOBRONCHIAL ULTRASONOGRAPHY; FEMALE; GENE EXPRESSION; GENETIC TRANSCRIPTION; HUMAN; HUMAN TISSUE; LUNG CANCER; LUNG GRANULOMA; LUNG SARCOIDOSIS; LYMPH NODE METASTASIS; MAJOR CLINICAL STUDY; MALE; MATHEMATICAL COMPUTING; MEDIASTINUM LYMPH NODE; MEDIASTINUM LYMPHADENOPATHY; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY AND SPECIFICITY; SUPPORT VECTOR MACHINE; TRANSBRONCHIAL ASPIRATION; TUBERCULOSIS; VERY ELDERLY; BRONCHOSCOPY; COMPARATIVE STUDY; COMPLICATION; ENDOSCOPIC ULTRASOUND GUIDED FINE NEEDLE BIOPSY; GENETICS; LYMPH NODE; LYMPHATIC DISEASES; MEDIASTINAL DISEASES; MEDIASTINUM; MIDDLE AGED; PATHOLOGY; PROCEDURES; SARCOIDOSIS, PULMONARY; YOUNG ADULT;

RNA; TRANSCRIPTOME;

ADULT; AGED; AGED, 80 AND OVER; BRONCHOSCOPY; ENDOSCOPIC ULTRASOUND-GUIDED FINE NEEDLE ASPIRATION; FEMALE; HUMANS; LYMPH NODES; LYMPHATIC DISEASES; MALE; MEDIASTINAL DISEASES; MEDIASTINUM; MIDDLE AGED; RNA; ROC CURVE; SARCOIDOSIS, PULMONARY; TRANSCRIPTOME; YOUNG ADULT;

EID: 84958087687     PISSN: 00123692     EISSN: 19313543     Source Type: Journal    
DOI: 10.1378/chest.15-0647     Document Type: Article

References (37)

1. Navani N, Spiro SG, Janes SM. Mediastinal staging of NSCLC with endoscopic and endobronchial ultrasound. Nat Rev Clin Oncol. 2009;6(5): 278-286.
2. Silvestri GA, Gonzalez AV, Jantz MA, et al. Methods for staging non-small cell lung cancer: diagnosis and management of lung cancer, 3rd ed: American College of Chest Physicians evidence-based clinical practice guidelines. Chest. 2013;143:e211S-e250S.
3. Agarwal R, Srinivasan A, Aggarwal AN, Gupta D. Efficacy and safety of convex probe EBUS-TBNA in sarcoidosis: a systematic review and meta-analysis. Respir Med. 2012;106(6):883-892.
4. Navani N, Molyneaux PL, Breen RA, et al. Utility of endobronchial ultrasoundguided transbronchial needle aspiration in patients with tuberculous intrathoracic lymphadenopathy: a multicentre study. Thorax. 2011;66(10):889-893.
5. Sun J, Teng J, Yang H, et al. Endobronchial ultrasound-guided transbronchial needle aspiration in diagnosing intrathoracic tuberculosis. Ann Thorac Surg. 2013;96(6):2021-2027.
6. Berry MP, Graham CM, McNab FW, et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature. 2010;466(7309): 973-977.
7. Pascual V, Chaussabel D, Banchereau J. A genomic approach to human autoimmune diseases. Annu Rev Immunol. 2010;28:535-571.
8. Ramilo O, Allman W, Chung W, et al. Gene expression patterns in blood leukocytes discriminate patients with acute infections. Blood. 2007;109(5): 2066-2077.
9. Bild AH, Yao G, Chang JT, et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature. 2006;439(7074):353-357.
10. Han SS, Kim WJ, Hong Y, et al. RNA sequencing identifies novel markers of non-small cell lung cancer. Lung Cancer. 2014;84(3):229-235.
11. Lee R, Cousins DJ, Ortiz-Zapater E, Breen R, McLean E, Santis G. Gene expression profiling of endobronchial ultrasound (EBUS)-derived cytological fine needle aspirates from hilar and mediastinal lymph nodes in non-small cell lung cancer. Cytopathology. 2013;24(6): 351-355.
12. Nakajima T, Zamel R, Anayama T, et al. Ribonucleic acid microarray analysis from lymph node samples obtained by endobronchial ultrasonography-guided transbronchial needle aspiration. Ann Thorac Surg. 2012;94(6):2097-2101.
13. Koth LL, Solberg OD, Peng JC, Bhakta NR, Nguyen CP, Woodruff PG. Sarcoidosis blood transcriptome reflects lung inflammation and overlaps with tuberculosis. Am J Respir Crit Care Med. 2011;184(10):1153-1163.
14. Maertzdorf J, Weiner J III, Mollenkopf HJ, et al. Common patterns and diseaserelated signatures in tuberculosis and sarcoidosis. Proc Natl Acad Sci U S A. 2012;109(20):7853-7858.
15. Bloom CI, Graham CM, Berry MP, et al. Transcriptional blood signatures distinguish pulmonary tuberculosis, pulmonary sarcoidosis, pneumonias and lung cancers. PLoS One. 2013;8(8):e70630.
16. Zissel G, Prasse A, Müller-Quernheim J. Sarcoidosis-immunopathogenetic concepts. Semin Respir Crit Care Med. 2007;28(1):3-14.
17. Hunninghake GW, Costabel U, Ando M, et al. ATS/ERS/WASOG statement on sarcoidosis. American Thoracic Society/European Respiratory Society/World Association of Sarcoidosis and other Granulomatous Disorders. Sarcoidosis Vasc Diffuse Lung Dis. 1999;16(2): 149-173.
18. Chain B, Bowen H, Hammond J, et al. Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays. BMC Bioinformatics. 2010;11:344.
19. Breuer K, Foroushani AK, Laird MR, et al. InnateDB: systems biology of innate immunity and beyond-recent updates and continuing curation. Nucleic Acids Res. 2013;41(database issue):D1228-D1233.
20. Tomlinson GS, Cashmore TJ, Elkington PT, et al. Transcriptional profiling of innate and adaptive human immune responses to mycobacteria in the tuberculin skin test. Eur J Immunol. 2011;41(11):3253-3260.
21. Cristianini N, Shawe-Taylor J. An Introduction to Support Vector Machines and Other Kernel-Based Learning Methods. New York, NY: Cambridge University Press; 2000.
22. Tetreault MP, Yang Y, Katz JP. Krüppellike factors in cancer. Nat Rev Cancer. 2013;13(10):701-713.
23. Henderson AR. The bootstrap: a technique for data-driven statistics. Using computerintensive analyses to explore experimental data. Clin Chim Acta. 2005;359(1-2):1-26.
24. Ambroise C, McLachlan GJ. Selection bias in gene extraction on the basis of microarray gene-expression data. Proc Natl Acad Sci U S A. 2002;99(10): 6562-6566.
25. Zissel G. Cellular activation in the immune response of sarcoidosis. Semin Respir Crit Care Med. 2014;35(3):307-315.
26. Debey S, Zander T, Brors B, Popov A, Eils R, Schultze JL. A highly standardized, robust, and cost-effective method for genome-wide transcriptome analysis of peripheral blood applicable to large-scale clinical trials. Genomics. 2006;87(5): 653-664.
27. Bossard MJ, Tomaszek TA, Thompson SK, et al. Proteolytic activity of human osteoclast cathepsin K. Expression, purification, activation, and substrate identification. J Biol Chem. 1996;271(21): 12517-12524.
28. Yagi M, Miyamoto T, Sawatani Y, et al. DC-STAMP is essential for cell-cell fusion in osteoclasts and foreign body giant cells. J Exp Med. 2005;202(3): 345-351.
29. Nagira M, Imai T, Hieshima K, et al. Molecular cloning of a novel human CC chemokine secondary lymphoidtissue chemokine that is a potent chemoattractant for lymphocytes and mapped to chromosome 9p13. J Biol Chem. 1997;272(31):19518-19524.
30. Mukhopadhyay S, Gal AA. Granulomatous lung disease: an approach to the differential diagnosis. Arch Pathol Lab Med. 2010;134(5):667-690.
31. Bargagli E, Maggiorelli C, Rottoli P. Human chitotriosidase: a potential new marker of sarcoidosis severity. Respiration. 2008;76(2):234-238.
32. Bargagli E, Margollicci M, Perrone A, et al. Chitotriosidase analysis in bronchoalveolar lavage of patients with sarcoidosis. Sarcoidosis Vasc Diffuse Lung Dis. 2007;24(1):59-64.
33. Bargagli E, Margollicci M, Nikiforakis N, et al. Chitotriosidase activity in the serum of patients with sarcoidosis and pulmonary tuberculosis. Respiration. 2007;74(5):548-552.
34. Valeyre D, Prasse A, Nunes H, Uzunhan Y, Brillet PY, Müller-Quernheim J. Sarcoidosis. Lancet. 2014;383(9923):1155-1167.
35. Navani N, Booth HL, Kocjan G, et al. Combination of endobronchial ultrasound-guided transbronchial needle aspiration with standard bronchoscopic techniques for the diagnosis of stage I and stage II pulmonary sarcoidosis. Respirology. 2011;16(3):467-472.
36. Tremblay A, Stather DR, Maceachern P, Khalil M, Field SK. A randomized controlled trial of standard vs endobronchial ultrasonography-guided transbronchial needle aspiration in patients with suspected sarcoidosis. Chest. 2009;136(2):340-346.
37. Navani N, Lawrence DR, Kolvekar S, et al; REMEDY Trial Investigators. Endobronchial ultrasound-guided transbronchial needle aspiration prevents mediastinoscopies in the diagnosis of isolated mediastinal lymphadenopathy: a prospective trial. Am J Respir Crit Care Med. 2012;186(3):255-260.