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Background Breast cancer (BC) is a complex heterogenous disease that is a leading cause of death in women. For patients with early stage disease following primary BC therapy, approximately 30% will develop metastatic BC (MBC). The median survival of MBC patients is ~ 2–3 yr. While the early detection and monitoring of BC progression have improved prognosis and reduced BC-related mortality, there is a lack of long-term surveillance strategies for monitoring patients for recurrence of MBC. The aim of our study was to identify non-invasive urinary biomarkers for detection and monitoring of MBC. Methods We have conducted a comparative label-free LC–MS/MS analysis of the urinary proteome of patients with MBC and healthy age-matched, sex-matched controls (HC). A hybrid quadrupole time of flight (Q-Tof™) mass spectrometer was used for urine analysis via liquid chromatography (LC) with tandem mass spectrometry (MS/MS). Retrospective analysis of urine samples from MBC and locally invasive breast cancer (IBC) patients as well as HC was conducted. Diagnostic accuracies of candidate markers were validated using independent training and validation sets according to the REMARK criteria. Results Using this approach, we have identified 212 urinary proteins of which 83 and 25 were unique to the MBC and HC groups, respectively. Upregulated proteins in the MBC cohort were associated with angiogenesis, Ca 2+ homeostasis, apoptosis, proteolysis, extracellular matrix regulation, cell adhesion and protein synthesis pathways. A specific non-invasive metastasis signature comprised of candidate biomarkers (urinary CALB1, S100A8, ZAG, VTN and TN) were validated and analyzed via monospecific ELISA assays. Urinary vitronectin (uVTN) levels correlated with disease status and were significantly higher in samples from MBC compared to those from IBC patients and HC. uVTN alone (cutoff > 500 ng/ml) could discriminate between HC and MBC groups ( AUC  = 0.782, P  < 0.001). Longitudinal analysis of samples from MBC patients indicated a strong correlation between uVTN levels and disease status. Conclusions Our findings suggest that uVTN is a promising and non-invasive biomarker for the diagnosis and monitoring of MBC. While future validation in larger cohorts should be done, these results identify a novel urinary protein that represents the first non-invasive diagnostic test for monitoring BC progression and recurrence.

Zusammenfassung Unter Verwendung eines quaternären UPLC-Chromatographiesystems wurde die effiziente Trennung eines heterogenen Gemischs aus einem synthetischen RNAi-Oligonukleotid und dessen unterbrochenen Sequenzen erzielt.

As column volumes continue to decrease, extra-column band broadening has become an increasingly important consideration when determining column performance. Combined contributions due to the injector and connecting tubing in a capillary LC system were measured and found to be larger than expected by Taylor-Aris theory. Variance from sigma-type and tau-type broadening was isolated from eluted peaks using the Foley-Dorsey Exponentially Modified Gaussian peak fitting model and confirmed with computational fluid dynamics. It was found that the tau-type contributions were the main cause for the excessive broadening because of poorly-swept volumes at the connection between the injector and tubing. To reduce tau-type contributions (and peak tailing), a timed pinch mode could be used for analyte injection.

A method for the analysis and characterization of therapeutic and diagnostic oligonucleotides has been developed using a combination of liquid chromatography and mass spectrometry (LC-MS). The optimized ion-pairing buffers permit a highly efficient separation of native and chemically modified antisense oligonucleotides (AS-ODNs) from their metabolites or failure synthetic products. The mobile phases were MS compatible, allowing for direct and sensitive analysis of components eluting from the column. The method was applied for the quantitation and characterization of AS-ODNs, including phosphorothioates and 2'-O-methyl-modified phosphorothioates. Tandem LC-MS analysis confirmed the identity of the oligonucleotide metabolites, failure products, the presence of protection groups not removed after synthesis, and the extent of depurination or phosphorothioate backbone oxidation.

There is an emerging interest in developing biosimilar monoclonal antibodies (MAbs). To avoid expensive clinical trials and shorten time to market, the biosimilar industry must establish that a developing product is, as much as possible, similar to a marketed innovator product through comprehensive analysis. Here, we demonstrate that ultra high pressure liquid chromatography (UHPLC) and mass spectrometry (MS) can be used routinely to characterize minor differences between a candidate biosimilar and an innovator IgG1 MAb. A two amino acid residue variance in the heavy chain sequence was detected by LC-MS intact protein mass measurement and located by tryptic peptide mapping with data independent acquisition LC-MS. Microheterogeneities due to N-linked glycosylation and chemical degradation were comprehensively catalogued and compared. The results show that complementary LC-MS methods can be used as a set of routine tools for rapid comparison of molecular similarity between a candidate biosimilar and a commercially available MAb. [PUBLICATION ABSTRACT]

In this paper, we describe denaturing and non-denaturing ion-pair reversed-phase liquid chromatography (RPLC) methods for analyzing small interfering ribonucleic acid (siRNA). Drug formulations consisting of one or two siRNA duplexes were analyzed in non-denaturing conditions at a low column temperature to separate intact duplexes from single-stranded oligonucleotide contaminants and quantify them. In a denaturing method, we used an elevated column temperature to ensure the denaturation of siRNA duplexes into their single-stranded oligonucleotide counterparts. The goal of the denaturing LC method was to investigate the impurities in daughter oligonucleotides in siRNA. A column with chemically modified C18 column hardware showed improvements in analytical performance for nucleic acids compared to a conventional C18 stainless-steel column with the same pore size.