Exploring metabolic profile differences between colorectal polyp patients and controls using seemingly unrelated regression

Journal of Proteome Research

Volumn 14, Issue 6, 2015, Pages 2492-2499

  Chen, Chen ^a   Deng, Lingli ^b   Wei, Siwei ^b   Nagana Gowda, G A ^b,d   Gu, Haiwei ^b   Chiorean, Elena G ^e,f   Abu Zaid, Mohammad ^e   Harrison, Marietta L ^c   Pekny, Joseph F ^b   Loehrer, Patrick J ^f   Zhang, Dabao ^a,e   Zhang, Min ^a,g,h   Raftery, Daniel ^b,e,i  

^a PURDUE UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

^c PURDUE UNIVERSITY   (United States)

^d XIAMEN UNIVERSITY   (China)

^e UNIVERSITY OF WASHINGTON   (United States)

^f INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^g CAPITAL MEDICAL UNIVERSITY   (China)

^h BEIJING INSTITUTE FOR BRAIN DISORDERS   (China)

ⁱ Fred Hutchinson Cancer Research Center   (United States)

Author keywords

colorectal polyp; metabolic profiling; metabolomics; NMR spectroscopy; seemingly unrelated regression

Indexed keywords

BIOLOGICAL MARKER; VALINE;

ADULT; AMINO ACID BLOOD LEVEL; ARTICLE; BODY MASS; CANCER RISK; CLINICAL ARTICLE; COLON CANCER; COLORECTAL POLYP; CONTROLLED STUDY; DEMOGRAPHY; DISEASE ASSOCIATION; FEMALE; HUMAN; MALE; METABOLITE; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; SEEMINGLY UNRELATED REGRESSION; SMOKING; STATISTICAL ANALYSIS; CASE CONTROL STUDY; COLON POLYP; METABOLISM; MIDDLE AGED; PATHOLOGY; RECTUM DISEASE;

CASE-CONTROL STUDIES; COLONIC POLYPS; FEMALE; HUMANS; MALE; MIDDLE AGED; RECTAL DISEASES;

EID: 84930606570     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00059     Document Type: Article

References (45)

1. Weitz, J.; Koch, M.; Debus, J.; Höhler, T.; Galle, P. R.; Büchler, M. W. Colorectal cancer Lancet 2005, 365 (9454) 153-165
2. Siegel, R.; Miller, K. D.; Jemal, A. Cancer statistics, 2015 CA-Cancer J. Clin. 2015, 65 (1) 5-29
3. Rex, D. K.; Johnson, D. A.; Anderson, J. C.; Schoenfeld, P. S.; Burke, C. A.; Inadomi, J. M. American college of gastroenterology guidelines for colorectal cancer screening 2008 Am. J. Gastroenterol. 2009, 104 (3) 739-750
4. Stegeman, I.; de Wijkerslooth, T. R.; Mallant-Hent, R. C.; de Groot, K.; Stroobants, A. K.; Fockens, P.; Mundt, M.; Bossuyt, P. M.; Dekker, E. Implementation of population screening for colorectal cancer by repeated Fecal Immunochemical Test (FIT): third round BMC Gastroenterol. 2012, 12-73
5. Imperiale, T. F.; Ransohoff, D. F.; Itzkowitz, S. H.; Levin, T. R.; Lavin, P.; Lidgard, G. P.; Ahlquist, D. A.; Berger, B. M. Multitarget stool DNA testing for colorectal-cancer screening N. Engl. J. Med. 2014, 370 (4) 1287-1297
6. Taylor, D. P.; Cannon-Albright, L. A.; Sweeney, C.; Williams, M. S.; Haug, P. J.; Mitchell, J. A.; Burt, R. W. Comparison of compliance for colorectal cancer screening and surveillance by colonoscopy based on risk Genet. Med. 2011, 13 (8) 737-743
7. Cancer Facts & Figures 2013; American Cancer Society: Atlanta, GA, 2013.
8. Warburg, O. On the origin of cancer cells Science 1956, 123, 309-314
9. Jain, M.; Nilsson, R.; Sharma, S.; Madhusudhan, N.; Kitami, T.; Souza, A. L.; Kafri, R.; Kirschner, M. W.; Clish, C. B.; Mootha, V. K. Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation Science 2012, 336 (6084) 1040-1044
10. Sreekumar, A.; Poisson, L. M.; Rajendiran, T. M.; Khan, A. P.; Cao, Q.; Yu, J.; Laxman, B.; Mehra, R.; Lonigro, R. J.; Li, Y.; Nyati, M. K.; Ahsan, A.; Kalyana-Sundaram, S.; Han, B.; Cao, X.; Byun, J.; Omenn, G. S.; Ghosh, D.; Pennathur, S.; Alexander, D. C.; Berger, A.; Shuster, J. R.; Wei, J. T.; Varambally, S.; Beecher, C.; Chinnaiyan, A. M. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression Nature 2009, 457 (7231) 910-914
11. Wise, D. R.; Thompson, C. B. Glutamine addiction: a new therapeutic target in cancer Trends Biochem. Sci. 2010, 35 (8) 427-433
12. Munoz-Pinedo, C.; El Mjiyad, N.; Ricci, J. E. Cancer metabolism: current perspectives and future directions Cell Death Dis. 2012, 3, e248
13. Gross, S.; Cairns, R. A.; Minden, M. D.; Driggers, E. M.; Bittinger, M. A.; Jang, H. G.; Sasaki, M.; Jin, S.; Schenkein, D. P.; Su, S. M.; Dang, L.; Fantin, V. R.; Mak, T. W. Cancer-associated metabolite 2-hydroxyglutarate accumulates in acute myelogenous leukemia with isocitrate dehydrogenase 1 and 2 mutations J. Exp. Med. 2010, 207 (2) 339-344
14. Patti, G. J.; Yanes, O.; Siuzdak, G. Innovation: Metabolomics: the apogee of the omics trilogy Nat. Rev. Mol. Cell Biol. 2012, 13 (4) 263-269
15. Gu, H.; Nagana Gowda, G. A.; Raftery, D. Metabolic profiling: are we en route to better diagnostic tests for cancer? Future Oncol. 2012, 8 (10) 1207-1210
16. Nagana Gowda, G. A.; Zhang, S.; Gu, H.; Asiago, V.; Shanaiah, N.; Raftery, D. Metabolomics based methods for early disease diagnostics Expert Rev. Mol. Diagn. 2008, 8 (5) 617-633
17. Scalbert, A.; Brennan, L.; Fiehn, O.; Hankemeier, T.; Kristal, B.; Ommen, B.; Pujos-Guillot, E.; Verheij, E.; Wishart, D.; Wopereis, S. Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research Metabolomics 2009, 5 (4) 435-458
18. Nicholson, J. K.; Holmes, E.; Kinross, J. M.; Darzi, A. W.; Takats, Z.; Lindon, J. C. Metabolic phenotyping in clinical and surgical environments Nature 2012, 491 (7424) 384-392
19. Fan, T.-M.; Lane, A. NMR-based stable isotope resolved metabolomics in systems biochemistry J. Biomol. NMR 2011, 49 (3-4) 267-280
20. Reaves, M. L.; Rabinowitz, J. D. Metabolomics in systems microbiology Curr. Opin. Biotechnol. 2011, 22 (1) 17-25
21. Bain, J. R.; Stevens, R. D.; Wenner, B. R.; Ilkayeva, O.; Muoio, D. M.; Newgard, C. B. Metabolomics applied to diabetes research: moving from information to knowledge Diabetes 2009, 58 (11) 2429-2443
22. Yanes, O.; Tautenhahn, R.; Patti, G. J.; Siuzdak, G. Expanding coverage of the metabolome for global metabolite profiling Anal. Chem. 2011, 83 (6) 2152-2161
23. Qiu, Y.; Cai, G.; Su, M.; Chen, T.; Zheng, X.; Xu, Y.; Ni, Y.; Zhao, A.; Xu, L. X.; Cai, S.; Jia, W. Serum metabolite profiling of human colorectal cancer using GC-TOFMS and UPLC-QTOFMS J. Proteome Res. 2009, 8 (10) 4844-4850
24. Nishiumi, S.; Kobayashi, T.; Ikeda, A.; Yoshie, T.; Kibi, M.; Izumi, Y.; Okuno, T.; Hayashi, N.; Kawano, S.; Takenawa, T.; Azuma, T.; Yoshida, M.; Novel Serum, A. Metabolomics-based diagnostic approach for colorectal cancer PLoS One 2012, 7 (7) e40459
25. Tan, B.; Qiu, Y.; Zou, X.; Chen, T.; Xie, G.; Cheng, Y.; Dong, T.; Zhao, L.; Feng, B.; Hu, X.; Xu, L. X.; Zhao, A.; Zhang, M.; Cai, G.; Cai, S.; Zhou, Z.; Zheng, M.; Zhang, Y.; Jia, W. Metabonomics identifies serum metabolite markers of colorectal cancer J. Proteome Res. 2013, 12 (6) 3000-3009
26. Denkert, C.; Budczies, J.; Weichert, W.; Wohlgemuth, G.; Scholz, M.; Kind, T.; Niesporek, S.; Noske, A.; Buckendahl, A.; Dietel, M.; Fiehn, O. Metabolite profiling of human colon carcinoma-deregulation of TCA cycle and amino acid turnover Mol. Cancer 2008, 7 (1) 72
27. Chan, E. C. Y.; Koh, P. K.; Mal, M.; Cheah, P. Y.; Eu, K. W.; Backshall, A.; Cavill, R.; Nicholson, J. K.; Keun, H. C. Metabolic profiling of human colorectal cancer using high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy and gas chromatography mass spectrometry (GC/MS) J. Proteome Res. 2008, 8 (1) 352-361
28. Ma, Y.-L.; Qin, H.-L.; Liu, W.-J.; Peng, J.-Y.; Huang, L.; Zhao, X.-P.; Cheng, Y.-Y. Ultra-high performance liquid chromatography-mass spectrometry for the metabolomic analysis of urine in colorectal cancer Dig. Dis. Sci. 2009, 54 (12) 2655-2662
29. Li, F.; Qin, X.; Chen, H.; Qiu, L.; Guo, Y.; Liu, H.; Chen, G.; Song, G.; Wang, X.; Li, F.; Guo, S.; Wang, B.; Li, Z. Lipid profiling for early diagnosis and progression of colorectal cancer using direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry Rapid Commun. Mass Spectrom. 2013, 27 (1) 24-34
30. Ritchie, S.; Ahiahonu, P.; Jayasinghe, D.; Heath, D.; Liu, J.; Lu, Y.; Jin, W.; Kavianpour, A.; Yamazaki, Y.; Khan, A.; Hossain, M.; Su-Myat, K.; Wood, P.; Krenitsky, K.; Takemasa, I.; Miyake, M.; Sekimoto, M.; Monden, M.; Matsubara, H.; Nomura, F.; Goodenowe, D. Reduced levels of hydroxylated, polyunsaturated ultra long-chain fatty acids in the serum of colorectal cancer patients: implications for early screening and detection. BMC Med. 2010, (8), 13.
31. Ritchie, S. A.; Tonita, J.; Alvi, R.; Lehotay, D.; Elshoni, H.; Myat, S.; McHattie, J.; Goodenowe, D. B. Low-serum GTA-446 anti-inflammatory fatty acid levels as a new risk factor for colon cancer Int. J. Cancer 2013, 132 (2) 355-362
32. Eisner, R.; Greiner, R.; Tso, V.; Wang, H.; Fedorak, R. N. A machine-learned predictor of colonic polyps based on urinary metabolomics Biomed. Res. Int. 2013, 2013, 303982
33. Zhu, J.; Djukovic, D.; Deng, L.; Gu, H.; Himmati, F.; Chiorean, E. G.; Raftery, D. Colorectal cancer detection using targeted serum metabolic profiling J. Proteome. Res. 2014, 13 (9) 4120-30
34. Zellner, A. An efficient method of estimating seemingly unrelated regressions and tests for aggregation bias J. Am. Stat. Assoc. 1962, 57 (298) 348-368
35. Aiken, L. S.; West, S. G. Multiple Regression: Testing and Interpreting Interactions; SAGE Publications, Inc.: Newbury Park, CA, 1991.
36. Krishnaiah, A. H.; Paruchuri, R., Eds.; Multivariate Analysis; Academic Press, Inc.: New York, 1971; p 1967.
37. Zhang, J.; Liu, L.; Wei, S.; Nagana Gowda, G. A.; Hammoud, Z.; Kesler, K. A.; Raftery, D. Metabolomics study of esophageal adenocarcinoma J. Thorac. Cardiovasc. Surg. 2011, 141, 469-475
38. Kohavi, R.; John, G. Wrappers for feature selection Artif. Intell. 1997, 97 (1-2) 273-324
39. Benjamini, Y.; Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing J. Royal Stat. Soc. B 1995, 57 (1) 289-300
40. Kanehisa, M.; Goto, S.; Kawashima, S.; Okuno, Y.; Hattori, M. The KEGG resource for deciphering the genome Nucleic Acids Res. 2004, 32, D277-D280
41. Saint-Pierre, A.; Kaufman, J. M.; Ostertag, A.; Cohen-Solal, M.; Boland, A.; Toye, K.; Zelenika, D.; Lathrop, M.; de Vernejoul, M. C.; Martinez, M. Bivariate association analysis in selected samples: application to a GWAS of two bone mineral density phenotypes in males with high or low BMD Eur. J. Hum Genet. 2011, 19 (6) 710-716
42. Carroll, R. J.; Midthune, D.; Freedman, L. S.; Kipnis, V. Seemingly unrelated measurement error models, with application to nutritional epidemiology Biometrics 2006, 62 (1) 75-84
43. Leichtle, A. B.; Nuoffer, J. M.; Ceglarek, U.; Kase, J.; Conrad, T.; Witzigmann, H.; Thiery, J.; Fiedler, G. M. Serum amino acid profiles and their alterations in colorectal cancer Metabolomics 2012, 8 (4) 643-653
44. Argilés, J.; Azcón-Bieto, J. The metabolic environment of cancer Mol. Cell. Biochem. 1988, 81 (1) 3-17
45. Miyagi, Y.; Higashiyama, M.; Gochi, A.; Akaike, M.; Ishikawa, T.; Miura, T.; Saruki, N.; Bando, E.; Kimura, H.; Imamura, F.; Moriyama, M.; Ikeda, I.; Chiba, A.; Oshita, F.; Imaizumi, A.; Yamamoto, H.; Miyano, H.; Horimoto, K.; Tochikubo, O.; Mitsushima, T.; Yamakado, M.; Okamoto, N. Plasma free amino acid profiling of five types of cancer patients and its application for early detection PLoS One 2011, 6 (9) e24143