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Expert Review of Proteomics Volume 13, 2016 - Issue 2
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Review

Crucial considerations for pipelines to validate circulating biomarkers for breast cancer

Radwa EwaishaCenter for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
,
Chelsea D. GawryletzDepartment of Medical Oncology, Mayo Clinic Arizona, Scottsdale, AZ, USA
&
Karen S. AndersonCenter for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA;Department of Medical Oncology, Mayo Clinic Arizona, Scottsdale, AZ, USACorrespondence[email protected]
Pages 201-211 | Received 21 Oct 2015, Accepted 10 Dec 2015, Published online: 04 Jan 2016

References

  • Papers of special note have been highlighted as:
  • • of interest
  • •• of considerable interest
  • Pernikarova V, Bouchal P. Targeted proteomics of solid cancers: from quantification of known biomarkers towards reading the digital proteome maps. Expert Rev Proteomics. 2015;12(6):1–17.
  • Boersema PJ, Geiger T, Wisniewski JR, et al. Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples. Mol Cell Proteomics. 2013;12(1):158–171.
  • Kroemer G, Senovilla L, Galluzzi L, et al. Natural and therapy-induced immunosurveillance in breast cancer. Nat Med. 2015;21(10):1128–1138.
  • Schwarzenbach H. Circulating nucleic acids as biomarkers in breast cancer. Breast Cancer Res: BCR. 2013;15(5):211.
  • Paoletti C, Hayes DF. Molecular testing in breast cancer. Annu Rev Med. 2014;65:95–110.
  • Gingras I, Salgado R, Ignatiadis M. Liquid biopsy: will it be the ‘magic tool’ for monitoring response of solid tumors to anticancer therapies? Curr Opin Oncol. 2015;27(6):560–567.
  • Dawson SJ, Tsui DW, Murtaza M, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013;368(13):1199–1209.
  • Garcia-Murillas I, Schiavon G, Weigelt B, et al. Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer. Sci Transl Med. 2015;7(302):302ra133.

• Tracking mutations in ctDNA was shown to correlate with minimal residual disease and identification of patients with high risk of relapse

  • O’Brien K, Rani S, Corcoran C, et al. Exosomes from triple-negative breast cancer cells can transfer phenotypic traits representing their cells of origin to secondary cells. Eur J Cancer. 2013;49(8):1845–1859.
  • O’Driscoll L. Expanding on exosomes and ectosomes in cancer. N Engl J Med. 2015;372(24):2359–2362.
  • Yu S, Cao H, Shen B, et al. Tumor-derived exosomes in cancer progression and treatment failure. Oncotarget. 2015;6(35):37151–37168.
  • Jiang ZF, Cristofanilli M, Shao ZM, et al. Circulating tumor cells predict progression-free and overall survival in Chinese patients with metastatic breast cancer, HER2-positive or triple-negative (CBCSG004): a multicenter, double-blind, prospective trial. Ann Oncol. 2013;24(11):2766–2772.
  • Liu MC. By the numbers: does circulating tumor cell enumeration have a role in metastatic breast cancer? J Clin Oncol. 2014;32(31):3479–3482.
  • Gunter MJ, Wang T, Cushman M, et al. Circulating adipokines and inflammatory markers and postmenopausal breast cancer risk. J Natl Cancer Inst. 2015;107(9):djv169.
  • Patel SK, Wong AL, Wong FL, et al. Inflammatory biomarkers, comorbidity, and neurocognition in women with newly diagnosed breast cancer. J Natl Cancer Inst. 2015;107(8):djv131.
  • Anderson KS, Sibani S, Wallstrom G, et al. Protein microarray signature of autoantibody biomarkers for the early detection of breast cancer. J Proteome Res. 2011;10(1):85–96.
  • Chapman C, Murray A, Chakrabarti J, et al. Autoantibodies in breast cancer: their use as an aid to early diagnosis. Ann Oncol. 2007;18(5):868–873.
  • Wang J, Figueroa JD, Wallstrom G, et al. Plasma autoantibodies associated with basal-like breast cancers. Cancer Epidemiol Biomarkers Prev. 2015;24(9):1332–1340.
  • Poste G. Bring on the biomarkers. Nature. 2011;469(7329):156–157.
  • Poste G, Compton CC, Barker AD. The national biomarker development alliance: confronting the poor productivity of biomarker research and development. Expert Rev Mol Diagn. 2015;15(2):211–218.

• This review summarizes the problems facing biomarker development identified by the National Biomarker Development Alliance, a nonprofit entity that aims at developing standards enabling rapid progress of biomarkers to the clinic

  • Van Poznak C, Somerfield MR, Bast RC, et al. Use of biomarkers to guide decisions on systemic therapy for women with metastatic breast cancer: American Society of Clinical Oncology Clinical practice guideline. J Clinical Oncol: Official J Am Soc Clin Oncol. 2015;33(24):2695–2704.
  • Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol. 2006;24(8):971–983.
  • Chen J, Liu QJ, Wang D, et al. Hepatoma upregulated protein expression is involved in the pathogenesis of human breast carcinogenesis. Oncol Lett. 2014;8(6):2543–2548.
  • Zeidan BA, Townsend PA, Garbis SD, et al. Clinical proteomics and breast cancer. Surgeon. 2015;13(5):271–278.
  • US Preventive Task Force. Available from: http://www.uspreventiveservicestaskforce.org.
  • Bevers TB, Anderson BO, Bonaccio E, et al. NCCN clinical practice guidelines in oncology: breast cancer screening and diagnosis. J Natl Compr Cancer Network: JNCCN. 2009;7(10):1060–1096.
  • Breast Cancer Risk Assessment Tool. Available from: http://www.cancer.gov/bcrisktool/.
  • Tice JA, Miglioretti DL, Li CS, et al. Breast density and benign breast disease: risk assessment to identify women at high risk of breast cancer. J Clinical Oncol: Official J Am Soc Clin Oncol. 2015;33(28):3137–3143.
  • Narod SA. BRCA mutations in the management of breast cancer: the state of the art. Nat Reviews Clin Oncology. 2010;7(12):702–707.
  • Chou C-P, Lewin JM, Chiang C-L, et al. Clinical evaluation of contrast-enhanced digital mammography and contrast enhanced tomosynthesis-Comparison to contrast-enhanced breast MRI. Eur J Radiol. 2015;84(12):2501–2508.
  • Garcia-Closas M, Couch FJ, Lindstrom S, et al. Genome-wide association studies identify four ER negative-specific breast cancer risk loci. Nat Genet. 2013;45(4):392–398, 398e1–2.
  • Michailidou K, Hall P, Gonzalez-Neira A, et al. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Nat Genet. 2013;45(4):353–361, 361e1–2.
  • Manchanda R, Legood R, Burnell M, et al. Cost-effectiveness of population screening for BRCA mutations in Ashkenazi jewish women compared with family history-based testing. J Natl Cancer Inst. 2015;107(1):380.
  • Harding C, Pompei F, Burmistrov D, et al. Breast cancer screening, incidence, and mortality across US counties. JAMA Intern Med. 2015;175(9):1483–1489.
  • Kirsh VA, Chiarelli AM, Edwards SA, et al. Tumor characteristics associated with mammographic detection of breast cancer in the Ontario breast screening program. J Natl Cancer Inst. 2011;103(12):942–950.
  • Opstal-van Winden AW, Krop EJ, Kåredal MH, et al. Searching for early breast cancer biomarkers by serum protein profiling of pre-diagnostic serum; a nested case-control study. BMC Cancer. 2011;11:381.
  • Riley CP, Zhang X, Nakshatri H, et al. A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples. J Transl Med. 2011;9:80.
  • Marks JR, Anderson KS, Engstrom P, et al. Construction and analysis of the NCI-EDRN breast cancer reference set for circulating markers of disease. Cancer Epidemiol Biomarkers Prev. 2015;24(2):435–441.

• This paper describes the construction and analysis of the NCI-Early Detection Research Network Breast Cancer Reference Set, a biorepository containing samples available for the research community upon request

  • Pietrowska M, Polanska J, Marczak L, et al. Mass spectrometry-based analysis of therapy-related changes in serum proteome patterns of patients with early-stage breast cancer. J Transl Med. 2010;8:66.
  • Bohm D, Keller K, Wehrwein N, et al. Serum proteome profiling of primary breast cancer indicates a specific biomarker profile. Oncol Rep. 2011;26(5):1051–1056.
  • Pepe MS, Feng Z, Janes H, et al. Pivotal evaluation of the accuracy of a biomarker used for classification or prediction: standards for study design. J Natl Cancer Inst. 2008;100(20):1432–1438.

•• This is the first publication to describe the PRoBE study design for biomarker research

  • Pepe MS, Li CI, Feng Z. Improving the quality of biomarker discovery research: the right samples and enough of them. Cancer Epidemiol Biomarkers Prev. 2015;24(6):944–950.
  • Pepe MS, Etzioni R, Feng Z, et al. Phases of biomarker development for early detection of cancer. J Natl Cancer Inst. 2001;93(14):1054–1061.
  • Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490(7418):61–70.
  • Skates SJ. A statistical challenge: developing tests for biomarker utility specific to the intended use. J Natl Cancer Inst. 2014;106(4):dju076.
  • Skates SJ, Gillette MA, LaBaer J, et al. Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies. J Proteome Res. 2013;12(12):5383–5394.

• The authors describe statistical design criteria for biomarker discovery and verification using proteomic approaches

• This is a study of the impact of tumor heterogeneity, and statistical modeling, of biomarker discovery and validation

  • Dash RC, Robb JA, Booker DL, et al. Biospecimens and biorepositories for the community pathologist. Arch Pathol Lab Med. 2012;136(6):668–678.
  • Robb JA, Gulley ML, Fitzgibbons PL, et al. A call to standardize preanalytic data elements for biospecimens. Arch Pathol Lab Med. 2014;138(4):526–537.
  • The Early Detection Research Network. [Internet; cited 2015 Dec 28]. Available from: http://edrn.nci.nih.gov/
  • Feng Z, Kagan J, Pepe M, et al. The early detection research network’s specimen reference sets: paving the way for rapid evaluation of potential biomarkers. Clin Chem. 2013;59(1):68–74.
  • Gonzalez RM, Daly DS, Tan R, et al. Plasma biomarker profiles differ depending on breast cancer subtype but RANTES is consistently increased. Cancer Epidemiol Biomarkers Prev. 2011;20(7):1543–1551.
  • Chan DS, Bandera EV, Greenwood DC, et al. Circulating C-reactive protein and breast cancer risk-systematic literature review and meta-analysis of prospective cohort studies. Cancer Epidemiol Biomarkers Prev. 2015;24(10):1439–1449.
  • Buas MF, Rho JH, Chai X, et al. Candidate early detection protein biomarkers for ER+/PR+ invasive ductal breast carcinoma identified using pre-clinical plasma from the WHI observational study. Breast Cancer Res Treat. 2015;153(2):445–454.
  • Li CI, Mirus JE, Zhang Y, et al. Discovery and preliminary confirmation of novel early detection biomarkers for triple-negative breast cancer using preclinical plasma samples from the women’s health initiative observational study. Breast Cancer Res Treat. 2012;135(2):611–618.

• This study identifies multiple potential biomarkers for the early detection of triple-negative breast cancer using pre-diagnostic plasmas

  • Pitteri SJ, Amon LM, Busald Buson T, et al. Detection of elevated plasma levels of epidermal growth factor receptor before breast cancer diagnosis among hormone therapy users. Cancer Res. 2010;70(21):8598–8606.
  • Amon LM, Pitteri SJ, Li CI, et al. Concordant release of glycolysis proteins into the plasma preceding a diagnosis of ER+ breast cancer. Cancer Res. 2012;72(8):1935–1942.
  • Jin H, Daly DS, Marks JR, et al. Oxidatively modified proteins as plasma biomarkers in breast cancer. Cancer Biomark. 2013;13(3):193–200.
  • Brauer HA, D’Arcy M, Libby TE, et al. Dermcidin expression is associated with disease progression and survival among breast cancer patients. Breast Cancer Res Treat. 2014;144(2):299–306.
  • Leth-Larsen R, Lund RR, Ditzel HJ. Plasma membrane proteomics and its application in clinical cancer biomarker discovery. Mol Cell Proteomics. 2010;9(7):1369–1382.
  • Zawadzka AM, Schilling B, Cusack MP, et al. Phosphoprotein secretome of tumor cells as a source of candidates for breast cancer biomarkers in plasma. Mol Cell Proteomics. 2014;13(4):1034–1049.
  • Gromov P, Gromova I, Bunkenborg J, et al. Up-regulated proteins in the fluid bathing the tumour cell microenvironment as potential serological markers for early detection of cancer of the breast. Mol Oncol. 2010;4(1):65–89.
  • Turtoi A, Dumont B, Greffe Y, et al. Novel comprehensive approach for accessible biomarker identification and absolute quantification from precious human tissues. J Proteome Res. 2011;10(7):3160–3182.
  • Haslene-Hox H, Tenstad O, Wiig H. Interstitial fluid-a reflection of the tumor cell microenvironment and secretome. Biochim Biophys Acta. 2013;1834(11):2336–2346.
  • Cheng J, Liu S, Zhang FF. Circulating biomarkers in breast cancer prognosis and survival: a systematic review. FASEB J. 2015;29(Suppl 1):906–921.
  • Anderson KS, Wong J, Polyak K, et al. Detection of psoriasin/S100A7 in the sera of patients with psoriasis. Br J Dermatol. 2009;160(2):325–332.
  • Vester-Christensen MB, Halim A, Joshi HJ, et al. Mining the O-mannose glycoproteome reveals cadherins as major O-mannosylated glycoproteins. Proc Natl Acad Sci U S A. 2013;110(52):21018–21023.
  • Ladd JJ, Chao T, Johnson MM, et al. Autoantibody signatures involving glycolysis and splicesome proteins precede a diagnosis of breast cancer among postmenopausal women. Cancer Res. 2013;73(5):1502–1513.
  • Katayama H, Boldt C, Ladd JJ, et al. An autoimmune response signature associated with the development of triple-negative breast cancer reflects disease pathogenesis. Cancer Res. 2015;75(16):3246–3254.
  • Lacombe J, Mange A, Bougnoux AC, et al. A multiparametric serum marker panel as a complementary test to mammography for the diagnosis of node-negative early-stage breast cancer and DCIS in young women. Cancer Epidemiol Biomarkers Prev. 2014;23(9):1834–1842.
  • Lu H, Ladd J, Feng Z, et al. Evaluation of known oncoantibodies, HER2, p53, and cyclin B1, in prediagnostic breast cancer sera. Cancer Prev Res (Phila). 2012;5(8):1036–1043.
  • Goufman EI, Iakovlev VN, Tikhonova NB, et al. Quantification of autoantibodies to plasminogen in plasma of patients with cancer. Cancer Biomark. 2015;15(3):281–287.
  • Maroun MC, Olivero O, Lipovich L, et al. Anti-centrosome antibodies in breast cancer are the expression of autoimmunity. Immunol Res. 2014;60(2–3):339–347.
  • Mohammed ME, Abdelhafiz K. Autoantibodies in the sera of breast cancer patients: antinuclear and anti-double stranded DNA antibodies as example. J Cancer Res Ther. 2015;11(2):341–344.
  • Lopez-Arias E, Aguilar-Lemarroy A, Felipe Jave-Suarez L, et al. Alpha 1-antitrypsin: a novel tumor-associated antigen identified in patients with early-stage breast cancer. Electrophoresis. 2012;33(14):2130–2137.
  • Bidard FC, Fehm T, Ignatiadis M, et al. Clinical application of circulating tumor cells in breast cancer: overview of the current interventional trials. Cancer Metastasis Rev. 2013;32(1–2):179–188.
  • Bidard FC, Mathiot C, Degeorges A, et al. Clinical value of circulating endothelial cells and circulating tumor cells in metastatic breast cancer patients treated first line with bevacizumab and chemotherapy. Ann Oncol. 2010;21(9):1765–1771.
  • Giuliano M, Giordano A, Jackson S, et al. Circulating tumor cells as early predictors of metastatic spread in breast cancer patients with limited metastatic dissemination. Breast Cancer Res. 2014;16(5):440.
  • Bidard FC, Peeters DJ, Fehm T, et al. Clinical validity of circulating tumour cells in patients with metastatic breast cancer: a pooled analysis of individual patient data. Lancet Oncol. 2014;15(4):406–414.
  • Peeters DJE, van Dam PJ, Van den Eynden GGM, et al. Detection and prognostic significance of circulating tumour cells in patients with metastatic breast cancer according to immunohistochemical subtypes. Br J Cancer. 2014;110(2):375–383.
  • Castle J, Shaker H, Morris K, et al. The significance of circulating tumour cells in breast cancer: A review. The Breast. 2014;23(5):552–560.
  • Melo SA, Sugimoto H, O’Connell JT, et al. Cancer exosomes perform cell-independent microRNA biogenesis and promote tumorigenesis. Cancer Cell. 2014;26(5):707–721.
  • Guzman N, Agarwal K, Asthagiri D, et al. Breast cancer-specific mir signature unique to extracellular vesicles includes “microRNA-like” tRNA fragments. Mol Cancer Res. 2015;13(5):891–901.
  • Andorfer CA, Necela BM, Thompson EA, et al. MicroRNA signatures: clinical biomarkers for the diagnosis and treatment of breast cancer. Trends Mol Med. 2011;17(6):313–319.
  • Jansson MD, Lund AH. MicroRNA and cancer. Mol Oncol. 2012;6(6):590–610.
  • Bertoli G, Cava C, Castiglioni I. MicroRNAs: new biomarkers for diagnosis, prognosis, therapy prediction and therapeutic tools for breast cancer. Theranostics. 2015;5(10):1122–1143.
  • Hu Z, Dong J, Wang LE, et al. Serum microRNA profiling and breast cancer risk: the use of miR-484/191 as endogenous controls. Carcinogenesis. 2012;33(4):828–834.
  • Jung EJ, Santarpia L, Kim J, et al. Plasma microRNA 210 levels correlate with sensitivity to trastuzumab and tumor presence in breast cancer patients. Cancer. 2012;118(10):2603–2614.
  • Kleivi Sahlberg K, Bottai G, Naume B, et al. A serum microRNA signature predicts tumor relapse and survival in triple-negative breast cancer patients. Clin Cancer Res. 2015;21(5):1207–1214.
  • Wu Q, Lu Z, Li H, et al. Next-generation sequencing of microRNAs for breast cancer detection. J Biomed Biotechnol. 2011;2011:597145.
  • Joosse SA, Muller V, Steinbach B, et al. Circulating cell-free cancer-testis MAGE-A RNA, BORIS RNA, let-7b and miR-202 in the blood of patients with breast cancer and benign breast diseases. Br J Cancer. 2014;111(5):909–917.
  • Sun Y, Wang M, Lin G, et al. Serum microRNA-155 as a potential biomarker to track disease in breast cancer. PLoS One. 2012;7(10):e47003.
  • Mishra S, Srivastava AK, Suman S, et al. Circulating miRNAs revealed as surrogate molecular signatures for the early detection of breast cancer. Cancer Lett. 2015;369(1):67–75.
  • Kelly H, Downing T, Tuite NL, et al. Cross platform standardisation of an experimental pipeline for use in the identification of dysregulated human circulating MiRNAs. PLoS One. 2015;10(9):e0137389.
  • Mangolini A, Ferracin M, Zanzi MV, et al. Diagnostic and prognostic microRNAs in the serum of breast cancer patients measured by droplet digital PCR. Biomark Res. 2015;3:12.
  • Jung K, Fleischhacker M, Rabien A. Cell-free DNA in the blood as a solid tumor biomarker–a critical appraisal of the literature. Clin Chim Acta. 2010;411(21–22):1611–1624.
  • Tripathy D, Rugo HS, Kaufman PA, et al. The SystHERs registry: an observational cohort study of treatment patterns and outcomes in patients with human epidermal growth factor receptor 2-positive metastatic breast cancer. BMC Cancer. 2014;14:307.
  • Board RE, Wardley AM, Dixon JM, et al. Detection of PIK3CA mutations in circulating free DNA in patients with breast cancer. Breast Cancer Res Treat. 2010;120(2):461–467.
  • Higgins MJ, Jelovac D, Barnathan E, et al. Detection of tumor PIK3CA status in metastatic breast cancer using peripheral blood. Clin Cancer Res. 2012;18(12):3462–3469.
  • Bettegowda C, Sausen M, Leary RJ, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014;6(224):224ra24.
  • Wittenberger T, Sleigh S, Reisel D, et al. DNA methylation markers for early detection of women’s cancer: promise and challenges. Epigenomics. 2014;6(3):311–327.
  • Avraham A, Uhlmann R, Shperber A, et al. Serum DNA methylation for monitoring response to neoadjuvant chemotherapy in breast cancer patients. Int J Cancer. 2012;131(7):E1166–72.

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