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Optics Express

Optics Express

  • Editor: C. Martijn de Sterke
  • Vol. 20, Iss. 20 — Sep. 24, 2012
  • pp: 22158–22171

Comparison of principal component analysis and biochemical component analysis in Raman spectroscopy for the discrimination of apoptosis and necrosis in K562 leukemia cells

Yi Hong Ong, Mayasari Lim, and Quan Liu  »View Author Affiliations

Optics Express, Vol. 20, Issue 20, pp. 22158-22171 (2012)

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Raman spectroscopy has been explored as a promising label-free technique in discriminating apoptosis and necrosis induced cell death in leukemia cells. In addition to Principal component analysis (PCA) as commonly employed in Raman data analysis, another less commonly used but powerful method is Biochemical Component Analysis (BCA). In BCA, a Raman spectrum is decomposed into the contributions from several known basic biochemical components, such as proteins, lipid, nucleic acids and glycogen groups etc. The differences in terms of classification accuracy and interpretability of resulting data between these two methods in Raman spectroscopy have not been systematically investigated to our knowledge. In this study, we utilized both methods to analyze the Raman spectra measured from live cells, apoptotic and necrotic leukemia cells. The comparison indicates that two methods yield comparable accuracy in sample classification when the numbers of basic components are equal. The changes in the contributions of biochemical components in BCA can be interpreted by cell biology principles in apoptosis and necrosis. In contrast, the contributions of most principle components in PCA are difficult to interpret except the first one. The capability of BCA to unveil fine biochemical changes in cell spectra and excellent accuracy in classification can impel the broad application of Raman spectroscopy in biological research.

© 2012 OSA

OCIS Codes
(070.4790) Fourier optics and signal processing : Spectrum analysis
(300.6450) Spectroscopy : Spectroscopy, Raman
(180.5655) Microscopy : Raman microscopy

ToC Category:
Medical Optics and Biotechnology

Original Manuscript: July 17, 2012
Revised Manuscript: September 5, 2012
Manuscript Accepted: September 6, 2012
Published: September 12, 2012

Virtual Issues
Vol. 7, Iss. 11 Virtual Journal for Biomedical Optics

Yi Hong Ong, Mayasari Lim, and Quan Liu, "Comparison of principal component analysis and biochemical component analysis in Raman spectroscopy for the discrimination of apoptosis and necrosis in K562 leukemia cells," Opt. Express 20, 22158-22171 (2012)

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  1. P. Chen, A. G. Shen, X. D. Zhou, and J. M. Hu, “Bio-Raman spectroscopy: a potential clinical analytical method assisting in disease diagnosis,” Anal. Methods 3(6), 1257–1269 (2011). [CrossRef]
  2. C. L. Zavaleta, B. R. Smith, I. Walton, W. Doering, G. Davis, B. Shojaei, M. J. Natan, and S. S. Gambhir, “Multiplexed imaging of surface enhanced Raman scattering nanotags in living mice using noninvasive Raman spectroscopy,” Proc. Natl. Acad. Sci. U.S.A. 106(32), 13511–13516 (2009). [CrossRef] [PubMed]
  3. N. Kunapareddy, J. P. Freyer, and J. R. Mourant, “Raman spectroscopic characterization of necrotic cell death,” J. Biomed. Opt. 13(5), 054002 (2008). [CrossRef] [PubMed]
  4. B. R. Lutz, C. E. Dentinger, L. N. Nguyen, L. Sun, J. W. Zhang, A. N. Allen, S. Chan, and B. S. Knudsen, “Spectral Analysis of Multiplex Raman Probe Signatures,” ACS Nano 2(11), 2306–2314 (2008). [CrossRef] [PubMed]
  5. J. R. Mourant, J. Dominguez, S. Carpenter, K. W. Short, T. M. Powers, R. Michalczyk, N. Kunapareddy, A. Guerra, and J. P. Freyer, “Comparison of vibrational spectroscopy to biochemical and flow cytometry methods for analysis of the basic biochemical composition of mammalian cells,” J. Biomed. Opt. 11(6), 064024 (2006). [CrossRef] [PubMed]
  6. J. R. Mourant, K. W. Short, S. Carpenter, N. Kunapareddy, L. Coburn, T. M. Powers, and J. P. Freyer, “Biochemical differences in tumorigenic and nontumorigenic cells measured by Raman and infrared spectroscopy,” J. Biomed. Opt. 10(3), 031106 (2005). [CrossRef] [PubMed]
  7. A. G. Ryder, “Classification of narcotics in solid mixtures using Principal Component Analysis and Raman spectroscopy,” J. Forensic Sci. 47(2), 275–284 (2002). [PubMed]
  8. B. G. M. Vandeginste, D. L. Massart, L. M. C. Buydens, S. De Jong, P. J. Lewi, and J. Smeyers-Verbeke, Handbook of Chemometrics and Qualimetrics (Elsevier Science, 1998).
  9. H. Shinzawa, K. Awa, W. Kanematsu, and Y. Ozaki, “Multivariate data analysis for Raman spectroscopic imaging,” J. Raman Spectrosc. 40(12), 1720–1725 (2009). [CrossRef]
  10. K. E. Shafer-Peltier, A. S. Haka, M. Fitzmaurice, J. Crowe, J. Myles, R. R. Dasari, and M. S. Feld, “Raman microspectroscopic model of human breast tissue: implications for breast cancer diagnosis in vivo,” J. Raman Spectrosc. 33(7), 552–563 (2002). [CrossRef]
  11. D. Van de Sompel, E. Garai, C. Zavaleta, and S. S. Gambhir, “A Hybrid Least Squares and Principal Component Analysis Algorithm for Raman Spectroscopy,” PLoS ONE 7(6), e38850 (2012). [CrossRef] [PubMed]
  12. I. A. Boere, T. C. B. Schut, J. van den Boogert, R. W. F. de Bruin, and G. J. Puppels, “Use of fibre optic probes for detection of Barrett's epithelium in the rat oesophagus by Raman spectroscopy,” Vib. Spectrosc. 32(1), 47–55 (2003). [CrossRef]
  13. A. Molckovsky, L. M. Song, M. G. Shim, N. E. Marcon, and B. C. Wilson, “Diagnostic potential of near-infrared Raman spectroscopy in the colon: differentiating adenomatous from hyperplastic polyps,” Gastrointest. Endosc. 57(3), 396–402 (2003). [CrossRef] [PubMed]
  14. J. W. Chan, D. S. Taylor, S. M. Lane, T. Zwerdling, J. Tuscano, and T. Huser, “Nondestructive identification of individual leukemia cells by laser trapping Raman spectroscopy,” Anal. Chem. 80(6), 2180–2187 (2008). [CrossRef] [PubMed]
  15. H. Yao, Z. Tao, M. Ai, L. Peng, G. Wang, B. He, and Y.- Li, “Raman spectroscopic analysis of apoptosis of single human gastric cancer cells,” Vib. Spectrosc. 50(2), 193–197 (2009). [CrossRef]
  16. J. L. Pichardo-Molina, C. Frausto-Reyes, O. Barbosa-García, R. Huerta-Franco, J. L. González-Trujillo, C. A. Ramírez-Alvarado, G. Gutiérrez-Juárez, and C. Medina-Gutiérrez, “Raman spectroscopy and multivariate analysis of serum samples from breast cancer patients,” Lasers Med. Sci. 22(4), 229–236 (2007). [CrossRef] [PubMed]
  17. M. Moreno, L. Raniero, E. A. L. Arisawa, A. M. D. Santo, E. A. P. dos Santos, R. A. Bitar, and A. A. Martin, “Raman spectroscopy study of breast disease,” Theor. Chem. Acc. 125(3-6), 329–334 (2010). [CrossRef]
  18. G. Pyrgiotakis, O. E. Kundakcioglu, K. Finton, P. M. Pardalos, K. Powers, and B. M. Moudgil, “Cell death discrimination with Raman spectroscopy and support vector machines,” Ann. Biomed. Eng. 37(7), 1464–1473 (2009). [CrossRef] [PubMed]
  19. I. Notingher, S. Verrier, H. Romanska, A. E. Bishop, J. M. Polak, and L. L. Hench, “In situ characterisation of living cells by Raman spectroscopy,” Spectrosc. Int. J. 16(2), 43–51 (2002). [CrossRef]
  20. J. S. U. Hjorth, “Cross validation,” in Computer Intensive Statistical Methods: Validation, Model Selection, and Bootstrap (Chapman and Hall/CRC, 1993), 27–28.
  21. N. Stone, C. Kendall, J. Smith, P. Crow, and H. Barr, “Raman spectroscopy for identification of epithelial cancers,” Faraday Discuss. 126, 141–157, discussion 169–183 (2004). [CrossRef] [PubMed]
  22. A. Zoladek, F. C. Pascut, P. Patel, and I. Notingher, “Non-invasive time-course imaging of apoptotic cells by confocal Raman micro-spectroscopy,” J. Raman Spectrosc. 42(3), 251–258 (2011). [CrossRef]
  23. S. Malladi, M. Challa-Malladi, and S. B. Bratton, “Apoptosis,” in Comprehensive Toxicology (Second Edition), A. M. Editor-in-Chief: Charlene, ed. (Elsevier, 2010), 543–578.
  24. T. M. Sauerwald, A. Lewis, H. Dorai, and M. J. Betenbaugh, “Apoptosis: The Signaling Pathways and Their Control,” in Comprehensive Biotechnology (Second Edition), M.-Y. Editor-in-Chief: Murray, ed. (Academic Press, 2011), 483–494.
  25. A. Vaculova and B. Zhivotovsky, “Caspases: Determination of their activities in apoptotic cells,” in Programmed Cell Death, General Principles for Studying Cell Death, Pt A, R. KhosraviFar, Z. Zakeri, R. A. Lockshin, and M. Piacentini, eds. (Elsevier Academic Press Inc, 2008), 157–181.
  26. K. S. Saini and N. I. Walker, “Biochemical and molecular mechanisms regulating apoptosis,” Mol. Cell. Biochem. 178(1/2), 9–25 (1998). [CrossRef] [PubMed]
  27. M. Leist and P. Nicotera, “Cell Death: Apoptosis versus Necrosis,” in Primer on Cerebrovascular Diseases(Academic Press, 1997), 101–104.
  28. S. Elmore, “Apoptosis: a review of programmed cell death,” Toxicol. Pathol. 35(4), 495–516 (2007). [CrossRef] [PubMed]
  29. N. Kunapareddy, S. Carpenter, J. P. Freyer, and J. R. Mourant, “Biochemical characterization of cell-death via Raman spectroscopy - art. no. 60930V,” in Biomedical Vibrational Spectroscopy III: Advances in Research and Industry, A. MahadevanJansen, and W. H. Petrich, eds. (SPIE, 2006).
  30. S. Verrier, I. Notingher, J. M. Polak, and L. L. Hench, “In situ monitoring of cell death using Raman microspectroscopy,” Biopolymers 74(1-2), 157–162 (2004). [CrossRef] [PubMed]

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