Molecular classification of endometriosis and disease stage using high-dimensional genomic data

Endocrinology

Volumn 155, Issue 12, 2014, Pages 4986-4999

  Tamaresis, John S ^a,f   Irwin, Juan C ^a   Goldfien, Gabriel A ^a   Rabban, Joseph T ^b   Burney, Richard O ^c   Nezhat, Camran ^d   DePaolo, Louis V ^e   Giudice, Linda C ^a,b  

^a Center for Reproductive Sciences   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Madigan Healthcare System   (United States)

^d STANFORD UNIVERSITY   (United States)

^e EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^f STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ADULT; ARTIFICIAL INTELLIGENCE; CASE CONTROL STUDY; DECISION TREE; ENDOMETRIOSIS; ENDOMETRIUM; FEMALE; GENE EXPRESSION PROFILING; GENOMICS; HUMAN; MENSTRUAL CYCLE; METABOLISM; MIDDLE AGED; MOLECULAR DIAGNOSIS; SEVERITY OF ILLNESS INDEX;

ADULT; ARTIFICIAL INTELLIGENCE; CASE-CONTROL STUDIES; DECISION TREES; ENDOMETRIOSIS; ENDOMETRIUM; FEMALE; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MENSTRUAL CYCLE; MIDDLE AGED; MOLECULAR DIAGNOSTIC TECHNIQUES; SEVERITY OF ILLNESS INDEX; TRANSCRIPTOME;

EID: 84914126593     PISSN: 00137227     EISSN: 19457170     Source Type: Journal    
DOI: 10.1210/en.2014-1490     Document Type: Article

References (57)

1. Giudice LC. Clinical practice. Endometriosis. N Engl J Med. 2010;362(25):2389-2398.
2. Giudice LC, Kao LC. Endometriosis. Lancet. 2004;364(9447):1789-1799.
3. Sampson JA. Peritoneal endometriosis due to menstrual dissemination of endometrial tissue into the peritoneal cavity. Am J Obstet Gynecol. 1927;14:442-469.
4. Berkley KJ, Rapkin AJ, Papka RE. The pains of endometriosis. Science. 2005;308(5728):1587-1589.
5. Tokushige N, Markham R, Russell P, Fraser IS. Nerve fibres in peritoneal endometriosis. Hum Reprod. 2006;21(11):3001-3007.
6. Eskenazi B, Warner ML. Epidemiology of endometriosis. Obstet Gynecol Clin North Am. 1997;24(2):235-258.
7. Meuleman C, Vandenabeele B, Fieuws S, Spiessens C, Timmerman D, D'Hooghe T. High prevalence of endometriosis in infertile women with normal ovulation and normospermic partners. Fertil Steril. 2009;92(1):68-74.
8. Nnoaham KE, Hummelshoj L, Webster P, et al. Impact of endometriosis on quality of life and work productivity: a multicenter study across ten countries. Fertil Steril. 2011;96(2):366-373.e368.
9. Simoens S, Dunselman G, Dirksen C, et al. The burden of endometriosis: costs and quality of life of women with endometriosis and treated in referral centres. Hum Reprod. 2012;27(5):1292-1299.
10. Bulun SE. Endometriosis. N Engl J Med. 2009;360(3):268-279.
11. Hadfield R, Mardon H, Barlow D, Kennedy S. Delay in the diagnosis of endometriosis: a survey of women from the USA and the UK. Hum Reprod. 1996;11(4):878-880.
12. D'Hooghe TM, Debrock S. Endometriosis, retrograde menstruation and peritoneal inflammation in women and in baboons. Hum Reprod Update. 2002;8(1):84-88.
13. Ballard K, Lowton K, Wright J. What's the delay? A qualitative study of women's experiences of reaching a diagnosis of endometriosis. Fertil Steril. 2006;86(5):1296-1301.
14. Melin AS, Lundholm C, Malki N, Swahn ML, Sparèn P, Bergqvist A. Hormonal and surgical treatments for endometriosis and risk of epithelial ovarian cancer. Acta Obstet Gynecol Scand. 2013;92(5):546-554.
15. D'Hooghe TM, Mihalyi AM, Simsa P, et al. Why we need a noninvasive diagnostic test for minimal to mild endometriosis with a high sensitivity. Gynecol Obstet Invest. 2006;62(3):136-138.
16. Burney RO, Talbi S, Hamilton AE, et al. Gene expression analysis of endometrium reveals progesterone resistance and candidate susceptibility genes in women with endometriosis. Endocrinology. 2007;148(8):3814-3826.
17. Kao LC, Germeyer A, Tulac S, et al. Expression profiling of endometrium from women with endometriosis reveals candidate genes for disease-based implantation failure and infertility. Endocrinology. 2003;144(7):2870-2881.
18. May KE, Villar J, Kirtley S, Kennedy SH, Becker CM. Endometrial alterations in endometriosis: a systematic review of putative biomarkers. Hum Reprod Update. 2011;17(5):637-653.
19. Matsuzaki S, Canis M, Vaurs-Barriere C, Boespflug-Tanguy O, Dastugue B, Mage G. DNA micro array analysis of gene expression in eutopic endometrium from patients with deep endometriosis using laser capture microdissection. Fertil Steril. 2005;84(suppl 2):1180-1190.
20. Sherwin JR, Sharkey AM, Mihalyi A, Simsa P, Catalano RD, D'Hooghe TM. Global gene analysis of late secretory phase, eutopic endometrium does not provide the basis for a minimally invasive test of endometriosis. Hum Reprod. 2008;23:1063-1068.
21. Revised American Society for Reproductive Medicine classification of endometriosis: 1996. Fertil Steril. 1997;67(5):817-821.
22. Noyes RW, Hertig AT, Rock J. Dating the endometrial biopsy. Am J Obstet Gynecol. 1975;122(2):262-263.
23. Talbi S, Hamilton AE, Vo KC, et al. Molecular phenotyping of human endometrium distinguishes menstrual cycle phases and underlying biological processes in normo-ovulatory women. Endocrinology. 2006;147(3):1097-1121.
24. Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc. 2004;99(468):909-917.
25. Tibshirani R, Hastie T. Margin trees for high-dimensional classification. J Mach Learn Res. 2007;8:637-652.
26. Pepe MS, Longton G, Anderson GL, Schummer M. Selecting differentially expressed genes from microarray experiments. Biometrics. 2003;59(1):133-142.
27. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3.
28. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci USA. 2005;102(38):13544-13549.
29. Spitzer TL, Rojas A, Zelenko Z, et al. Perivascular human endometrial mesenchymal stem cells express pathways relevant to self-renewal, lineage specification, and functional phenotype. Biol Reprod. 2012;86(2):58.
30. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3(6):1101-1108.
31. Rorabacher DB. Statistical treatment for rejection of deviant values: critical values of Dixon's "Q" parameter and related subrange ratios at the 95% confidence level. Anal Chem. 1991;63(2):139-146.
32. Lee S. Mistakes in validating the accuracy of a prediction classifier in high-dimensional but small-sample microarray data. Stat Methods Med Res. 2008;17(6):635-642.
33. Simon R. Roadmap for developing and validating therapeutically relevant genomic classifiers. J Clin Oncol. 2005;23(29):7332-7341.
34. Altmäe S, Esteban FJ, Stavreus-Evers A, et al. Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium. Hum Reprod Update. 2014;20(1):12-28.
35. Afshar Y, Hastings J, Roqueiro D, Jeong JW, Giudice LC, Fazleabas. Changes in eutopic endometrial gene expression during the progression of experimental endometriosis in the baboon, Papio anubis. Biol Reprod. 2013;88(2):44-53.
36. Aghajanova L, Giudice LC. Molecular evidence for differences in endometrium in severe versus mild endometriosis. Reprod Sci. 2011;18(3):229-251.
37. Fassbender A, Vodolazkaia A, Saunders P, et al. Biomarkers of endometriosis. Fertil Steril. 2013;99(4):1135-1145.
38. Fassbender A, Waelkens E, Verbeeck N, et al. Proteomics analysis of plasma for early diagnosis of endometriosis. Obstet Gynecol. 2012;119(2 pt 1):276-285.
39. May KE, Conduit-Hulbert SA, Villar J, Kirtley S, Kennedy SH, Becker CM. Peripheral biomarkers of endometriosis: a systematic review. Hum Reprod Update. 2010;16(6):651-674.
40. Zheng N, Pan C, Liu W. New serum biomarkers for detection of endometriosis using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Int Med Res. 2011;39(4):1184-1192.
41. Rogers PA, D'Hooghe TM, Fazleabas A, et al. Defining future directions for endometriosis research: workshop report from the 2011 World Congress of Endometriosis In Montpellier, France. Reprod Sci. 2013;20(5):483-499.
42. Zhang X, Lu B, Huang X, Xu H, Zhou C, Lin J. Innervation of endometrium and myometrium in women with painful adenomyosis and uterine fibroids. Fertil Steril. 2010;94(2):730-737.
43. Vodolazkaia A, El-Aalamat Y, Popovic D, et al. Evaluation of a panel of 28 biomarkers for the non-invasive diagnosis of endometriosis. Hum Reprod. 2012;27(9):2698-2711.
44. Pan Q, Luo X, Toloubeydokhti T, Chegini N. The expression profile of micro-RNA in endometrium and endometriosis and the influence of ovarian steroids on their expression. Mol Hum Reprod. 2007;13(11):797-806.
45. Fassbender A, Rahmioglu N, Vitonis AF, et al for the WERF EPHect Working Group. WERF Endometriosis Phenome and Biobanking Harmonization Project (EPHect): IV. Tissue collection, processing and storage in endometriosis research [published online September 22, 2014]. Fertil Steril. doi:10.1016/j.fertnstert.2014.07.1209.
46. Becker CM, Laufer MR, Stratton P, et al for the WERF EPHect Working Group. WERF Endometriosis Phenome and Biobanking Harmonization Project (EPHect): I. Surgical phenotype data collection in endometriosis research [published online August 21, 2014]. Fertil Steril. doi:10.1016/j.fertnstert.2014.07.709.
47. Fassbender A, Verbeeck N, Börnigen D, et al. Combined mRNA microarray and proteomic analysis of eutopic endometrium of women with and without endometriosis. Hum Reprod. 2012;27(7):2020-2029.
48. El-Kasti MM, Wright C, Fye HK, Roseman F, Kessler BM, Becker CM. Urinary peptide profiling identifies a panel of putative biomarkers for diagnosing and staging endometriosis. Fertil Steril. 2011;95(4):1261-1266.e1-e6.
49. Hu E, Mueller E, Oliviero S, Papaioannou VE, Johnson R, Spiegelman BM. Targeted disruption of the c-fos gene demonstrates c-fos-dependent and -independent pathways for gene expression stimulated by growth factors or oncogenes. EMBO J. 1994;13(13):3094-3103.
50. Kirkland JL, Murthy L, Stancel GM. Progesterone inhibits the estrogen-induced expression of c-fos messenger ribonucleic acid in the uterus. Endocrinology. 1992;130(6):3223-3230.
51. Hastings JM, Jackson KS, Mavrogianis PA, Fazleabas AT. The estrogen early response gene FOS is altered in a baboon model of endometriosis. Biol Reprod. 2006;75(2):176-182.
52. Kim SH, Han SY, Azam T, Yoon DY, Dinarello CA. Interleukin-32: a cytokine and inducer of TNFα. Immunity. 2005;22(1):131-142.
53. Menten P, Wuyts A, Van Damme J. Macrophage inflammatory protein-1. Cytokine Growth Factor Rev. 2002;13(6):455-481.
54. Janeway C. Immunobiology: The Immune System in Health and Disease. 6th ed. New York, NY: Garland Science; 2005.
55. Rackow BW, Jorgensen E, Taylor HS. Endometrial polyps affect uterine receptivity. Fertil Steril. 2011;95(8):2690-2692.
56. Meyer WR, Castelbaum AJ, Somkuti S, et al. Hydrosalpinges adversely affect markers of endometrial receptivity. Hum Reprod. 1997;12(7):1393-1398.
57. Rackow BW, Taylor HS. Submucosal uterine leiomyomas have a global effect on molecular determinants of endometrial receptivity. Fertil Steril. 2010;93(6):2027-2034.