A circulating extracellular vesicles-based novel screening tool for colorectal cancer revealed by shotgun and data-independent acquisition mass spectrometry

References

• Arnold M, Sierra MS, Laversanne M, et al. Global patterns and trends in colorectal cancer incidence and mortality. Gut. 2017;66:683–13.
   PubMed Web of Science ®Google Scholar
• Brodt P. Role of the microenvironment in liver metastasis: from pre- to prometastatic niches. Clin Cancer Res off J Am Assoc Cancer Res. 2016;22:5971–5982.
   PubMed Web of Science ®Google Scholar
• Shao Y, Chen T, Zheng X, et al. Colorectal cancer-derived small extracellular vesicles establish an inflammatory premetastatic niche in liver metastasis. Carcinogenesis. 2018;39:1368–1379.
   PubMed Web of Science ®Google Scholar
• Doubeni CA, Gabler NB, Wheeler CM, et al. Timely follow-up of positive cancer screening results: A systematic review and recommendations from the PROSPR Consortium. CA Cancer J Clin. 2018;68:199–216.
   PubMed Web of Science ®Google Scholar
• Issa IA, Noureddine M. Colorectal cancer screening: an updated review of the available options. World J Gastroenterol. 2017;23:5086–5096.
   PubMed Web of Science ®Google Scholar
• Yanez-Mo M, Siljander PR, Andreu Z, et al. Biological properties of extracellular vesicles and their physiological functions. J Extracell Vesicles. 2015;4:27066.
   PubMed Web of Science ®Google Scholar
• Tkach M, Thery C. Communication by extracellular vesicles: where we are and where we need to go. Cell. 2016;164:1226–1232.
   PubMed Web of Science ®Google Scholar
• Melo SA, Luecke LB, Kahlert C, et al. Glypican-1 identifies cancer exosomes and detects early pancreatic cancer. Nature. 2015;523:177–182.
   PubMed Web of Science ®Google Scholar
• Li J, Li B, Ren C, et al. The clinical significance of circulating GPC1 positive exosomes and its regulative miRNAs in colon cancer patients. Oncotarget. 2017;8:101189–101202.
   Google Scholar
• Chen IH, Xue L, Hsu CC, et al. Phosphoproteins in extracellular vesicles as candidate markers for breast cancer. Proc Natl Acad Sci U S A. 2017;114:3175–3180.
   PubMed Web of Science ®Google Scholar
• Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis. 2014;35:3430–3440.
   PubMed Web of Science ®Google Scholar
• Gillet LC, Navarro P, Tate S, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics. 2012;11:O111 016717.
   PubMed Web of Science ®Google Scholar
• Guo T, Kouvonen P, Koh CC, et al. Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nat Med. 2015;21:407–413.
   PubMed Web of Science ®Google Scholar
• Reubsaet L, Sweredoski MJ, Moradian A. Data-independent acquisition for the Orbitrap Q Exactive HF: a tutorial. J Proteome Res. 2019;18:803–813.
   PubMed Web of Science ®Google Scholar
• Zhu T, Zhu Y, Xuan Y, et al. DPHL: A pan-human protein mass spectrometry library for robust biomarker discovery. bioRxiv. 2020;2020(2):03.931329.
   Google Scholar
• Peterson AC, Russell JD, Bailey DJ, et al. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol Cell Proteomics. 2012;11:1475–1488.
   PubMed Web of Science ®Google Scholar
• Bourmaud A, Gallien S, Domon B. Parallel reaction monitoring using quadrupole-Orbitrap mass spectrometer: principle and applications. Proteomics. 2016;16:2146–2159.
   PubMed Web of Science ®Google Scholar
• Wu J, Wang Y, Xu X, et al. Transcriptional activation of FN1 and IL11 by HMGA2 promotes the malignant behavior of colorectal cancer. Carcinogenesis. 2016;37:511–521.
   PubMed Web of Science ®Google Scholar
• Sun L, Hu S, Yu L, et al. Serum haptoglobin as a novel molecular biomarker predicting colorectal cancer hepatic metastasis. Int J Cancer. 2016;138:2724–2731.
   Web of Science ®Google Scholar
• Fan NJ, Chen HM, Song W, et al. Macrophage mannose receptor 1 and S100A9 were identified as serum diagnostic biomarkers for colorectal cancer through a label-free quantitative proteomic analysis. Cancer Biomarkers. 2016;16:235–243.
   Web of Science ®Google Scholar
• Palumbo JS, Talmage KE, Massari JV, et al. Platelets and fibrin(ogen) increase metastatic potential by impeding natural killer cell-mediated elimination of tumor cells. Blood. 2005;105:178–185.
   PubMed Web of Science ®Google Scholar
• Rost HL, Rosenberger G, Navarro P, et al. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol. 2014;32:219–223.
   PubMed Web of Science ®Google Scholar
• Malvezzi M, Carioli G, Bertuccio P, et al. European cancer mortality predictions for the year 2018 with focus on colorectal cancer. Ann Oncol. 2018;29:1016–1022.
   Web of Science ®Google Scholar
• Giuliano M, Shaikh A, Lo HC, et al. Perspective on circulating tumor cell clusters: why it takes a village to metastasize. Cancer Res. 2018;78:845–852.
   PubMed Web of Science ®Google Scholar
• Merker JD, Oxnard GR, Compton C, et al. Circulating tumor DNA analysis in patients with cancer: american society of clinical oncology and college of American pathologists joint review. J Clin Oncol. 2018;36:1631–1641.
   PubMed Web of Science ®Google Scholar
• Matsumura T, Sugimachi K, Iinuma H, et al. Exosomal microRNA in serum is a novel biomarker of recurrence in human colorectal cancer. Br J Cancer. 2015;113:275–281.
   PubMed Web of Science ®Google Scholar
• Liu Y, Gu Y, Han Y, et al. Tumor exosomal RNAs promote lung pre-metastatic niche formation by activating alveolar epithelial TLR3 to recruit neutrophils. Cancer Cell. 2016;30:243–256.
   PubMed Web of Science ®Google Scholar
• Wei Z, Batagov AO, Schinelli S, et al. Coding and noncoding landscape of extracellular RNA released by human glioma stem cells. Nat Commun. 2017;8:1145.
   PubMed Web of Science ®Google Scholar
• Kawamura M, Toiyama Y, Tanaka K, et al. Can circulating MicroRNAs become the test of choice for colorectal cancer? Curr Colorectal Cancer Rep. 2014;10:403–410.
   Google Scholar
• Lai X, Wang M, McElyea SD, et al. A microRNA signature in circulating exosomes is superior to exosomal glypican-1 levels for diagnosing pancreatic cancer. Cancer Lett. 2017;393:86–93.
   PubMed Web of Science ®Google Scholar
• Lewis JM, Vyas AD, Qiu Y, et al. Integrated analysis of exosomal protein biomarkers on alternating current electrokinetic chips enables rapid detection of pancreatic cancer in patient blood. ACS Nano. 2018;12:3311–3320.
   Web of Science ®Google Scholar
• Fujita Y, Yoshioka Y, Ochiya T. Extracellular vesicle transfer of cancer pathogenic components. Cancer Sci. 2016;107:385–390.
   Web of Science ®Google Scholar
• Megger DA, Pott LL, Ahrens M, et al. Comparison of label-free and label-based strategies for proteome analysis of hepatoma cell lines. Biochim Biophys Acta. 2014;1844:967–976.
   PubMed Web of Science ®Google Scholar
• Savitski MM, Mathieson T, Zinn N, et al. Measuring and managing ratio compression for accurate iTRAQ/TMT quantification. J Proteome Res. 2013;12:3586–3598.
   PubMed Web of Science ®Google Scholar
• Choi DS, Lee JM, Park GW, et al. Proteomic analysis of microvesicles derived from human colorectal cancer cells. J Proteome Res. 2007;6:4646–4655.
   PubMed Web of Science ®Google Scholar
• de Wit M, Kant H, Piersma SR, et al. Colorectal cancer candidate biomarkers identified by tissue secretome proteome profiling. J Proteomics. 2014;99:26–39.
   PubMed Web of Science ®Google Scholar
• Peinado H, Zhang H, Matei IR, et al. Pre-metastatic niches: organ-specific homes for metastases. Nat Rev Cancer. 2017;17:302–317.
   PubMed Web of Science ®Google Scholar
• Obata J, Tanaka N, Mizuno R, et al. Plasma fibrinogen level: an independent prognostic factor for disease-free survival and cancer-specific survival in patients with localised renal cell carcinoma. BJU Int. 2016;118:598–603.
   Web of Science ®Google Scholar
• Sun ZQ, Han XN, Wang HJ, et al. Prognostic significance of preoperative fibrinogen in patients with colon cancer. World J Gastroenterol. 2014;20:8583–8591.
   PubMed Web of Science ®Google Scholar
• Simpson-Haidaris PJ, Rybarczyk B. Tumors and fibrinogen. The role of fibrinogen as an extracellular matrix protein. Ann N Y Acad Sci. 2001;936:406–425.
   PubMed Web of Science ®Google Scholar
• Hunter T. Signaling–2000 and beyond. Cell. 2000;100:113–127.
   PubMed Web of Science ®Google Scholar
• Kabuyama Y, Resing KA, Ahn NG. Applying proteomics to signaling networks. Curr Opin Genet Dev. 2004;14:492–498.
   PubMed Web of Science ®Google Scholar
• Son HJ, Park JW, Chang HJ, et al. Preoperative plasma hyperfibrinogenemia is predictive of poor prognosis in patients with nonmetastatic colon cancer. Ann Surg Oncol. 2013;20:2908–2913.
   PubMed Web of Science ®Google Scholar
• Lee JH, Hyun JH, Kim DY, et al. The role of fibrinogen as a predictor in preoperative chemoradiation for rectal cancer. Ann Surg Oncol. 2015;22:209–215.
   PubMed Web of Science ®Google Scholar
• Geyer PE, Holdt LM, Teupser D, et al. Revisiting biomarker discovery by plasma proteomics. Mol Syst Biol. 2017;13:942.
   PubMed Web of Science ®Google Scholar
• Brenes A, Hukelmann J, Bensaddek D, et al. Multibatch TMT reveals false positives, batch effects and missing values. Mol Cell Proteomics. 2019;18:1967–1980.
   PubMed Web of Science ®Google Scholar
• Wunsch BH, Smith JT, Gifford SM, et al. Nanoscale lateral displacement arrays for the separation of exosomes and colloids down to 20 nm. Nat Nanotechnol. 2016;11:936–940.
   PubMed Web of Science ®Google Scholar
• Karttunen J, Heiskanen M, Navarro-Ferrandis V, et al. Precipitation-based extracellular vesicle isolation from rat plasma co-precipitate vesicle-free microRNAs. J Extracell Vesicles. 2019;8:1555410.
   PubMed Web of Science ®Google Scholar