Microfluidic enrichment of small proteins from complex biological mixture on nanoporous silica chip

Abstract

The growing field of miniaturized diagnostics is hindered by a lack of pre-analysis treatments that are capable of processing small sample volumes for the detection of low concentration analytes in a high-throughput manner. This letter presents a novel, highly efficient method for the extraction of low-molecular weight ͑LMW͒ proteins from biological fluids, represented by a mixture of standard proteins, using integrated microfluidic systems. We bound a polydimethylsiloxane layer patterned with a microfluidic channel onto a well-defined nanoporous silica substrate. Using rapid, pressure-driven fractionation steps, this system utilizes the size-exclusion properties of the silica nanopores to remove high molecular weight proteins while simultaneously isolating and enriching LMW proteins present in the biological sample. The introduction of the microfluidic component offers important advantages such as high reproducibility, a simple user interface, controlled environment, the ability to process small sample volumes, and precise quantification. This solution streamlines high-throughput proteomics research on many fronts and may find broad acceptance and application in clinical diagnostics and point of care detection. © 2011 American Institute of Physics. ͓doi:10.1063/1.3528237͔Despite advances in the analysis of blood metabolites, the histochemical evaluation of tissue biopsies, and improvements in imaging approaches, early detection and diagnosis of human disease still suffers from severe limitations. A promising strategy to overcome this conundrum is the detection of molecular signatures from readily available body fluids. 1 However, the onset of most diseases cannot be unequivocally identified on the basis of a single biomarker. 2-4 Considerable attention has been devoted to the development of proteomic methods for the simultaneous, quantitative detection of multiple protein and peptide biomarkers ͑signature profiles͒ using mass spectrometry ͑MS͒. 5-7 A critical aspect of the development of MS-based proteomics and peptidomics is the extraordinarily broad assortment of molecular species in blood, with concentrations ranging over more than ten orders of magnitude. 8 This dynamic complexity is a significant barrier to the detection of disease-related peptides, many of which are present in trace amounts and are hidden within a background of highly abundant, nonrelevant proteins. Several strategies for sample treatment prior to MS analysis have been developed to address these limitations, 9,10 including conventional two-dimensional gel electrophoresis, 11 prefractionation processes, 12,13 depletion of highabundance proteins, 14,15 coated magnetic bead-based extractions, 16 and beads equalization. 17,18 Despite these substantial advances, many of the listed techniques are prone to experimental variability, limited reproducibility, unwieldy handling procedures, protein instability during sample a͒ These authors contributed equally to this work.

Circulating Proteolytic Products of Carboxypeptidase N for Early Detection of Breast Cancer

“…Briefly, low-molecular weight peptides are captured and preserved on NPS thin films, separating them from often overwhelming, high-molecular weight proteins/peptides prior to mass spectrometry analysis. Analysis by mass spectrometry can provide not only the quantitative information for multiple peptides species in a single sample, but also helps to identify their sequence information (24–26, 28–30). The in vivo expression of CPN in tissues (evaluated by immunohistochemistry (IHC)) or blood (by immunoblotting) is correlated to the presence or quantity (see protocols in supplemental information).…”

Monitoring the progression of metastatic breast cancer on nanoporous silica chips

“…While conventional chemotherapy and radiation therapy are initially effective in controlling breast cancer growth, patients frequently relapse over time. We have developed nanoporous silica chips to capture LMW serum peptides and proteins [21][22][23][24][25][26]. In our study, we used nanoporous silica chips to isolate LMW proteins and peptides from the serum of MDA-MB-231 lung metastatic cancer mice.…”

Clinical Predictive Circulating Peptides in Rectal Cancer Patients Treated with Neoadjuvant Chemoradiotherapy

“…NSCs produced at the Department of Nanomedicine of The Methodist Hospital Research Institute, Houston, TX (Bouamrani et al, ; Hu et al, ; Hu et al, ) were used for peptides harvesting from plasma and desalting procedures. Fifteen μl of plasma were mixed with 4 μl of 25% acetonitrile (ACN) and 1 microliter of 5% trifluoroacetic acid (TFA), both from Sigma–Aldrich, St. Louis, MO and incubated at room temperature for 30 min.…”