Influence of biospecimen variables on proteomic biomarkers in breast cancer

Clinical Cancer Research

Volumn 20, Issue 14, 2014, Pages 3870-3883

  Meric Bernstam, Funda ^a   Akcakanat, Argun ^a   Chen, Huiqin ^a   Sahin, Aysegul ^a   Tarco, Emily ^a   Carkaci, Selin ^a,b   Adrada, Beatriz E ^a   Singh, Gopal ^a   Do, Kim Anh ^a   Garces, Zerzhinski M ^a   Mittendorf, Elizabeth ^a   Babiera, Gildy ^a   Bedrosian, Isabelle ^a   Hwang, Rosa ^a   Krishnamurthy, Savitri ^a   Symmans, William F ^a   Gonzalez Angulo, Ana Maria ^a   Mills, Gordon B ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; GLYCOGEN SYNTHASE KINASE 3ALPHA; INITIATION FACTOR 4E BINDING PROTEIN 1; MAMMALIAN TARGET OF RAPAMYCIN; MITOGEN ACTIVATED PROTEIN KINASE KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE KINASE 2; PHOSPHATIDYLINOSITOL 3 KINASE; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PROGESTERONE RECEPTOR; PROTEIN KINASE B; S6 KINASE; STEM CELL FACTOR; PROTEOME; TUMOR MARKER;

ADULT; AGE DISTRIBUTION; ANALYTICAL PARAMETERS; ARTICLE; BIOSPECIMEN VARIABLE; BREAST BIOPSY; BREAST CANCER; CANCER ADJUVANT THERAPY; COLD ISCHEMIA; COMPARATIVE STUDY; CONTROLLED STUDY; ENZYME ACTIVATION; ENZYME PHOSPHORYLATION; EX VIVO STUDY; FINE NEEDLE ASPIRATION BIOPSY; HUMAN; HUMAN CELL; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; IN VIVO STUDY; INTRATUMORAL HETEROGENEITY; LARGE CORE NEEDLE BIOPSY; MAJOR CLINICAL STUDY; MASTECTOMY; ONCOLOGICAL PARAMETERS; PRIORITY JOURNAL; PROSPECTIVE STUDY; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEOMICS; REVERSE PHASE PROTEIN ARRAY; SIGNAL TRANSDUCTION; TUMOR CELLULARITY; TUMOR VOLUME; BREAST TUMOR; FEMALE; METABOLISM; PATHOLOGY;

BIOMARKERS, TUMOR; BREAST NEOPLASMS; FEMALE; HUMANS; PHOSPHATIDYLINOSITOL 3-KINASES; PROTEOME; SIGNAL TRANSDUCTION; TUMOR BURDEN;

EID: 84904400245     PISSN: 10780432     EISSN: 15573265     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-13-1507     Document Type: Article

References (28)

1. McAuliffe PF, Meric-Bernstam F, Mills GB, Gonzalez-Angulo AM. Deciphering the role of PI3K/Akt/mTOR pathway in breast cancer biology and pathogenesis. Clin Breast Cancer 2010;10 Suppl 3:S59-65.
2. Baker AF, Dragovich T, Ihle NT, Williams R, Fenoglio-Preiser C, Powis G. Stability of phosphoprotein as a biological marker of tumor signaling. Clin Cancer Res 2005;11:4338-40. (Pubitemid 40825621)
3. Pinhel IF, Macneill FA, Hills MJ, Salter J, Detre S, A'Hern R, et al. Extreme loss of immunoreactive p-Akt and p-Erk1/2 during routine fixation of primary breast cancer. Breast Cancer Res 2010;12:R76.
4. Spruessel A, Steimann G, Jung M, Lee SA, Carr T, Fentz AK, et al. Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. BioTechniques 2004;36:1030-7. (Pubitemid 38747367)
5. Yachida S, Jones S, Bozic I, Antal T, Leary R, Fu B, et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 2010;467:1114-7.
6. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012;366:883-92.
7. Cabioglu N, Hunt KK, Sahin AA, Kuerer HM, Babiera GV, Singletary SE, et al. Role for intraoperative margin assessment in patients undergoing breast-conserving surgery. Ann Surg Oncol 2007;14:1458-71. (Pubitemid 46536814)
8. Hatzis C, Sun H, Yao H, Hubbard RE, Meric-Bernstam F, Babiera GV, et al. Effects of tissue handling on RNA integrity and microarray measurements from resected breast cancers. J Natl Cancer Inst 2011;103:1871-83.
9. Hennessy BT, Lu Y, Gonzalez-Angulo AM, Carey MS, Myhre S, Ju Z, et al. A technical assessment of the utility of reverse phase protein arrays for the study of the functional proteome in non-microdissected human breast cancers. Clin Proteom 2010;6:129-51.
10. Meric-Bernstam F, Akcakanat A, Chen H, Do KA, Sangai T, Adkins F, et al. PIK3CA/PTEN mutations and Akt activation as markers of sensitivity to allosteric mTOR inhibitors. Clin Cancer Res 2012;18:1777-89.
11. Dudoit S, Yang YH. Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In:Parmigiani G, Garrett ES, Irizarry RA, Zeger SL, editors. The analysis of gene expression data: methods and software. New York: Springer; 2002.
12. Yang YH, Dudoit S, Luu P, Speed TP. Normalization for cDNA microarray data. In:Bittner ML, Chen Y, Dorsel AN, Dougherty ER, editors. Microarrays: optical technologies and informatics: SPIE - International Society for Optical Engine; 2001.
13. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002;30:e15.
14. Best DJ, Roberts DE. Algorithm AS 89. The upper tail probabilities of Spearman's rho. Appl Stat 1975;24:377-79.
15. Hollander M, Wolfe DA. Nonparametric statistical methods. New York: John Wiley & Sons; 1973.
16. Landis JR, Koch GG. The measurement of observer agreement for categorical data. Biometrics 1977;33:159-74. (Pubitemid 8054849)
17. Hu J, He X, Baggerly KA, Coombes KR, Hennessy BT, Mills GB. Non-parametric quantification of protein lysate arrays. Bioinformatics (Oxford, England) 2007;23:1986-94. (Pubitemid 47299840)
18. Symmans WF, Ayers M, Clark EA, Stec J, Hess KR, Sneige N, et al. Total RNA yield and microarray gene expression profiles from fine-needle aspiration biopsy and core-needle biopsy samples of breast carcinoma. Cancer 2003;97:2960-71. (Pubitemid 36676249)
19. Gewinner C, Wang ZC, Richardson A, Teruya-Feldstein J, Etemadmoghadam D, Bowtell D, et al. Evidence that inositol polyphosphate 4-phosphatase type II is a tumor suppressor that inhibits PI3K signaling. Cancer Cell 2009;16:115-25.
20. Meric-Bernstam F, Gonzalez-Angulo AM. Targeting the mTOR signaling network for cancer therapy. J Clin Oncol 2009;27:2278-87.
21. Arnedos M, Nerurkar A, Osin P, A'Hern R, Smith IE, Dowsett M. Discordance between core needle biopsy (CNB) and excisional biopsy (EB) for estrogen receptor (ER), progesterone receptor (PgR) and HER2 status in early breast cancer (EBC). Ann Oncol 2009;20:1948-52.
22. Li S, Yang X, Zhang Y, Fan L, Zhang F, Chen L, et al. Assessment accuracy of core needle biopsy for hormone receptors in breast cancer: a meta-analysis. Breast Cancer Res Treat 2012;135:325-34.
23. Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, et al. Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Mol Cell Proteomics 2014 May 7. [Epub ahead of print]
24. + advanced breast cancer (BC) with activated PI3K/mTOR pathway: exploratory biomarker observations from the BOLERO-3 trial. European Cancer Congress. Amsterdam, the Netherlands; 2013. p. Abstract LBA16.
25. Gonzalez-Angulo AM, Hennessy BT, Meric-Bernstam F, Sahin A, Liu W, Ju Z, et al. Functional proteomics can define prognosis and predict pathologic complete response in patients with breast cancer. Clin Proteomics 2011;8:11.
26. Mueller C, Decarvalho AC, Mikkelsen T, Lehman NL, Calvert V, Espina V, et al. Glioblastoma cell enrichment is critical for analysis of phosphorylated drug targets and proteomic-genomic correlations. Cancer Res 2014;74:818-28.
27. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 2012;490:61-70.
28. Akbani R, Ng PKS, Werner H, Shahmoradgoli M, Zhang F, Ju Z, et al. A pan-cancer proteomic perspective on The Cancer Genome Atlas. Nat Commun 2014; 29:3887.