The potential of circulating nucleic acids as components of companion diagnostics for predicting and monitoring chemotherapy response

References

• Duffy MJ. Role of tumor markers in patients with solid cancers: a critical review. Eur J Intern Med 2007;18(3):175-84
   PubMed Web of Science ®Google Scholar
• Philip R, Carrington L, Chan M. US FDA perspective on challenges in co-developing in vitro companion diagnostics and targeted cancer therapeutics. Bioanalysis 2011;3(4):383-9
   PubMed Web of Science ®Google Scholar
• Schwarzenbach H, Hoon DS, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer 2011;11(6):426-37
   PubMed Web of Science ®Google Scholar
• Stroun M, Maurice P, Vasioukhin V, et al. The origin and mechanism of circulating DNA. Ann N Y Acad Sci 2000;906:161-8
   PubMed Web of Science ®Google Scholar
• Arroyo JD, Chevillet JR, Kroh EM, et al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci USA 2011;108(12):5003-8
   PubMed Web of Science ®Google Scholar
• Orozco AF, Lewis DE. Flow cytometric analysis of circulating microparticles in plasma. Cytometry A 2010;77(6):502-14
   PubMed Web of Science ®Google Scholar
• Schwarzenbach H, Nishida N, Calin GA, et al. Clinical relevance of circulating cell-free microRNAs in cancer. Nat Rev Clin Oncol 2014;11(3):145-56
   PubMed Web of Science ®Google Scholar
• Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009;136(2):215-33
   PubMed Web of Science ®Google Scholar
• Angulo B, Lopez-Rios F, Gonzalez D. A new generation of companion diagnostics: cobas BRAF, KRAS and EGFR mutation detection tests. Expert Rev Mol Diagn 2014;14(5):517-24
   PubMed Web of Science ®Google Scholar
• Diehl F, Li M, Dressman D, et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci USA 2005;102(45):16368-73
   PubMed Web of Science ®Google Scholar
• Cooke S, Campbell P. Circulating DNA and next-generation sequencing. Recent Results Cancer Res Fortschritte der Krebsforschung. Progres dans les recherches sur le cancer 2012;195:143-9
   Google Scholar
• Murtaza M, Dawson SJ, Tsui DW, et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 2013;497(7447):108-12
   PubMed Web of Science ®Google Scholar
• Pinto JL, Fonseca FL, Marsicano SR, et al. Systemic chemotherapy-induced microsatellite instability in the mononuclear cell fraction of women with breast cancer can be reproduced in vitro and abrogated by amifostine. J Pharm Pharmacol 2010;62(7):931-4
   PubMed Web of Science ®Google Scholar
• Maier J, Lange T, Kerle I, et al. Detection of mutant free circulating tumor DNA in the plasma of patients with gastrointestinal stromal tumor harboring activating mutations of CKIT or PDGFRA. Clin Cancer Res 2013;19(17):4854-67
   PubMed Web of Science ®Google Scholar
• Spindler KL, Pallisgaard N, Andersen RF, et al. Gemcitabine and capecitabine for heavily pre-treated metastatic colorectal cancer patients a phase II and translational research study. Anticancer Res 2014;34(2):845-50
   PubMed Web of Science ®Google Scholar
• Spindler KL, Pallisgaard N, Andersen RF, et al. Changes in mutational status during third-line treatment for metastatic colorectal cancer-Results of consecutive measurement of cell free DNA, KRAS and BRAF in the plasma. Int J Cancer 2014;135(9):2215-22
   PubMed Web of Science ®Google Scholar
• Sakai K, Horiike A, Irwin DL, et al. Detection of epidermal growth factor receptor T790M mutation in plasma DNA from patients refractory to epidermal growth factor receptor tyrosine kinase inhibitor. Cancer Sci 2013;104(9):1198-204
   PubMed Web of Science ®Google Scholar
• Nakamura T, Sueoka-Aragane N, Iwanaga K, et al. A noninvasive system for monitoring resistance to epidermal growth factor receptor tyrosine kinase inhibitors with plasma DNA. J Thorac Oncol 2011;6(10):1639-48
   PubMed Web of Science ®Google Scholar
• Yam I, Lam DC, Chan K, et al. EGFR array: uses in the detection of plasma EGFR mutations in non-small cell lung cancer patients. J Thorac Oncol 2012;7(7):1131-40
   PubMed Web of Science ®Google Scholar
• Mack PC, Holland WS, Burich RA, et al. EGFR mutations detected in plasma are associated with patient outcomes in erlotinib plus docetaxel-treated non-small cell lung cancer. J Thorac Oncol 2009;4(12):1466-72
   PubMed Web of Science ®Google Scholar
• Kuang Y, Rogers A, Yeap BY, et al. Noninvasive detection of EGFR T790M in gefitinib or erlotinib resistant non-small cell lung cancer. Clin Cancer 2009;15(8):2630-6
   PubMed Web of Science ®Google Scholar
• Oxnard GR, Paweletz CP, Kuang Y, et al. Noninvasive detection of response and resistance in EGFR-mutant lung cancer using quantitative next-generation genotyping of cell-free plasma DNA. Clin Cancer 2014;20(6):1698-705
   PubMed Web of Science ®Google Scholar
• Wang S, An T, Wang J, et al. Potential clinical significance of a plasma-based KRAS mutation analysis in patients with advanced non-small cell lung cancer. Clin Cancer Res 2010;16(4):1324-30
   PubMed Web of Science ®Google Scholar
• Salkeni MA, Zarzour A, Ansay TY, et al. Detection of EGFRvIII mutant DNA in the peripheral blood of brain tumor patients. J Neurooncol 2013;115(1):27-35
   PubMed Web of Science ®Google Scholar
• Sharma G, Mirza S, Parshad R, et al. DNA methylation of circulating DNA: a marker for monitoring efficacy of neoadjuvant chemotherapy in breast cancer patients. Tumour Biol 2012;33(6):1837-43
   PubMedGoogle Scholar
• Chen KG, Sikic BI. Molecular pathways: regulation and therapeutic implications of multidrug resistance. Clin Cancer Res 2012;18(7):1863-9
   PubMed Web of Science ®Google Scholar
• Sharma G, Mirza S, Parshad R, et al. CpG hypomethylation of MDR1 gene in tumor and serum of invasive ductal breast carcinoma patients. Clin Biochem 2010;43(4-5):373-9
   PubMed Web of Science ®Google Scholar
• Ramirez JL, Salazar MF, Gupta J, et al. Methylation patterns and chemosensitivity in NSCLC. Adv Exp Med Biol 2006;587:195-209
   PubMedGoogle Scholar
• Fiegl H, Millinger S, Mueller-Holzner E, et al. Circulating tumor-specific DNA: a marker for monitoring efficacy of adjuvant therapy in cancer patients. Cancer Res 2005;65(4):1141-5
   PubMed Web of Science ®Google Scholar
• Gifford G, Paul J, Vasey PA, et al. The acquisition of hMLH1 methylation in plasma DNA after chemotherapy predicts poor survival for ovarian cancer patients. Clin Cancer Res 2004;10(13):4420-6
   PubMed Web of Science ®Google Scholar
• Kong W, Yang H, He L, et al. MicroRNA-155 is regulated by the transforming growth factor beta/Smad pathway and contributes to epithelial cell plasticity by targeting RhoA. Mol Cell Biol 2008;28(22):6773-84
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Chen J, Wang W, Zhang Y, et al. Predicting distant metastasis and chemoresistance using plasma miRNAs. Med Oncol 2014;31(1):799
   PubMed Web of Science ®Google Scholar
• Muller V, Gade S, Steinbach B, et al. Changes in serum levels of miR-21, miR-210, and miR-373 in HER2-positive breast cancer patients undergoing neoadjuvant therapy: a translational research project within the Geparquinto trial. Breast Cancer Res Treat 2014;147(1):61-8
   PubMed Web of Science ®Google Scholar
• Wang H, Tan G, Dong L, et al. Circulating MiR-125b as a marker predicting chemoresistance in breast cancer. PLoS One 2012;7(4):e34210
   PubMed Web of Science ®Google Scholar
• Cui EH, Li HJ, Hua F, et al. Serum microRNA 125b as a diagnostic or prognostic biomarker for advanced NSCLC patients receiving cisplatin-based chemotherapy. Acta Pharmacol Sin 2013;34(2):309-13
   PubMed Web of Science ®Google Scholar
• Freres P, Josse C, Bovy N, et al. Neoadjuvant chemotherapy in breast cancer patients induces miR-34a and miR-122 expression. J Cell Physiol 2014. [Epub ahead of print]
   Google Scholar
• Lowe SW, Bodis S, McClatchey A, et al. p53 status and the efficacy of cancer therapy in vivo. Science 1994;266(5186):807-10
   PubMed Web of Science ®Google Scholar
• Tazawa H, Tsuchiya N, Izumiya M, et al. Tumor-suppressive miR-34a induces senescence-like growth arrest through modulation of the E2F pathway in human colon cancer cells. Proc Natl Acad Sci USA 2007;104(39):15472-7
   PubMed Web of Science ®Google Scholar
• Zhang J, Zhang K, Bi M, et al. Circulating microRNA expressions in colorectal cancer as predictors of response to chemotherapy. Anticancer Drugs 2014;25(3):346-52
   PubMed Web of Science ®Google Scholar
• Ohyashiki K, Umezu T, Yoshizawa S, et al. Clinical impact of down-regulated plasma miR-92a levels in non-Hodgkin’s lymphoma. PLoS One 2011;6(2):e16408
   PubMed Web of Science ®Google Scholar
• Huang Y, Yang YB, Zhang XH, et al. MicroRNA-21 gene and cancer. Med Oncol 2013;30(1):376
   PubMed Web of Science ®Google Scholar
• Liu R, Chen X, Du Y, et al. Serum microRNA expression profile as a biomarker in the diagnosis and prognosis of pancreatic cancer. Clin Chem 2012;58(3):610-18
   PubMed Web of Science ®Google Scholar
• Wang P, Zhuang L, Zhang J, et al. The serum miR-21 level serves as a predictor for the chemosensitivity of advanced pancreatic cancer, and miR-21 expression confers chemoresistance by targeting FasL. Mol Oncol 2013;7(3):334-45
   PubMed Web of Science ®Google Scholar
• Lin HM, Castillo L, Mahon KL, et al. Circulating microRNAs are associated with docetaxel chemotherapy outcome in castration-resistant prostate cancer. Br J Cancer 2014;110(10):2462-71
   PubMed Web of Science ®Google Scholar
• Summerer I, Niyazi M, Unger K, et al. Changes in circulating microRNAs after radiochemotherapy in head and neck cancer patients. Radiat Oncol 2013;8:296
   PubMed Web of Science ®Google Scholar
• Tanaka K, Miyata H, Yamasaki M, et al. Circulating miR-200c levels significantly predict response to chemotherapy and prognosis of patients undergoing neoadjuvant chemotherapy for esophageal cancer. Ann Surg Oncol 2013;20(Suppl 3):S607-15
   PubMed Web of Science ®Google Scholar
• Ji J, Yu L, Yu Z, et al. Development of a miR-26 companion diagnostic test for adjuvant interferon-alpha therapy in hepatocellular carcinoma. Int J Biol Sci 2013;9(3):303-12
   PubMed Web of Science ®Google Scholar
• Shi MM. Technologies for individual genotyping: detection of genetic polymorphisms in drug targets and disease genes. Am J Pharmacogenomics 2002;2(3):197-205
   PubMedGoogle Scholar
• Hindson BJ, Ness KD, Masquelier DA, et al. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem 2011;83(22):8604-10
   PubMed Web of Science ®Google Scholar
• 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):311-27
   PubMed Web of Science ®Google Scholar
• Chen C, Ridzon DA, Broomer AJ, et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005;33(20):e179
   PubMed Web of Science ®Google Scholar
• Pritchard CC, Cheng HH, Tewari M. MicroRNA profiling: approaches and considerations. Nat Rev Genet 2012;13(5):358-69
   PubMed Web of Science ®Google Scholar
• Dong H, Lei J, Ding L, et al. MicroRNA: function, detection, and bioanalysis. Chem Rev 2013
   Google Scholar
• Kukita Y, Uchida J, Oba S, et al. Quantitative identification of mutant alleles derived from lung cancer in plasma cell-free DNA via anomaly detection using deep sequencing data. PLoS One 2013;8(11):e81468
   PubMed Web of Science ®Google Scholar
• Baudhuin LM, Donato LJ, Uphoff TS. How novel molecular diagnostic technologies and biomarkers are revolutionizing genetic testing and patient care. Expert Rev Mol Diagn 2012;12(1):25-37
   PubMed Web of Science ®Google Scholar
• Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008;26(10):1135-45
   PubMed Web of Science ®Google Scholar
• Hafner M, Renwick N, Brown M, et al. RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA 2011;17(9):1697-712
   PubMed Web of Science ®Google Scholar
• Joosse SA, Pantel K. Biologic challenges in the detection of circulating tumor cells. Cancer Res 2013;73(1):8-11
   PubMed Web of Science ®Google Scholar
• van de Stolpe A, den Toonder JM. Circulating tumor cells: what is in it for the patient? A vision towards the future. Cancers 2014;6(2):1195-207
   PubMed Web of Science ®Google Scholar
• Garcia-Olmo D, Garcia-Olmo DC. Functionality of circulating DNA: the hypothesis of genometastasis. Ann N Y Acad Sci 2001;945:265-75
   PubMed Web of Science ®Google Scholar
• Garcia-Olmo DC, Picazo MG, Garcia-Olmo D. Transformation of non-tumor host cells during tumor progression: theories and evidence. Expert Opin Biol Ther 2012;12(Suppl 1):S199-207
   PubMed Web of Science ®Google Scholar
• Azmi AS, Bao B, Sarkar FH. Exosomes in cancer development, metastasis, and drug resistance: a comprehensive review. Cancer Metastasis Rev 2013;32(3-4):623-42
   PubMed Web of Science ®Google Scholar
• Mandel P, Métais P. Les acides nucléiques du plasma sanguin chez l`homme. C R Acad Sci Paris 1948;142:241-3
   Google Scholar
• Swarup V, Rajeswari MR. Circulating (cell-free) nucleic acids–a promising, non-invasive tool for early detection of several human diseases. FEBS Lett 2007;581(5):795-9
   PubMed Web of Science ®Google Scholar
• Vlassov VV, Laktionov PP, Rykova EY. Extracellular nucleic acids. Bioessays 2007;29(7):654-67
   PubMed Web of Science ®Google Scholar
• Schwarzenbach H. Circulating nucleic acids and protease activities in blood of tumor patients. Expert Opin Biol Ther 2012;12(Suppl 1):S163-9
   Google Scholar
• Chiu RW, Lo YM. Clinical applications of maternal plasma fetal DNA analysis: translating the fruits of 15 years of research. Clin Chem Lab Med 2013;51(1):197-204
   PubMed Web of Science ®Google Scholar