Correction: Boronate affinity-based photoactivatable magnetic nanoparticles for the oriented and irreversible conjugation of Fc-fused lectins and antibodies.

[This corrects the article DOI: 10.1039/C9SC01613A.].

Integrating site-specific peptide reporters and targeted mass spectrometry enables rapid substrate-specific kinase assay at the nanogram cell level.

Dysregulation of phosphorylation-mediated signaling drives the initiation and progression of many diseases. A substrate-specific kinase assay capable of quantifying the altered site-specific phosphorylation of its phenotype-dependent substrates provides better specificity to monitor a disease state. We report a sensitive and rapid substrate-specific kinase assay by integrating site-specific peptide reporter and multiple reaction monitoring (MRM)-MS platform for relative and absolute quantification of substrate-specific kinase activity at the sensitivity of nanomolar kinase and nanogram cell lysate. Using non-small cell lung cancer as a proof-of-concept, three substrate peptides selected from constitutive phosphorylation in tumors (HDGF-S165, RALY-S135, and NRD1-S94) were designed to demonstrate the feasibility. The assay showed good accuracy (<15% nominal deviation) and reproducibility (<15% CV). In PC9 cells, the measured activity for HDGF-S165 was 3.2 ± 0.2 fmol µg-1 min-1, while RALY-S135 and NRD1-S94 showed 4- and 20-fold higher activity at the sensitivity of 25 ng and 5 ng lysate, respectively, suggesting different endogenous kinases for each substrate peptide. Without the conventional shotgun phosphoproteomics workflow, the overall pipeline from cell lysate to MS data acquisition only takes 3 h. The multiplexed analysis revealed differences in the phenotype-dependent substrate phosphorylation profiles across six NSCLC cell lines and suggested a potential association of HDGF-S165 and NRD1-S94 with TKI resistance. With the ease of design, sensitivity, accuracy, and reproducibility, this approach may offer rapid and sensitive assays for targeted quantification of the multiplexed substrate-specific kinase activity of small amounts of sample.

Boronate affinity-based photoactivatable magnetic nanoparticles for the oriented and irreversible conjugation of Fc-fused lectins and antibodies.

The utilization of immuno-magnetic nanoparticles (MNPs) for the selective capture, enrichment, and separation of specific glycoproteins from complicated biological samples is appealing for the discovery of disease biomarkers. Herein, MNPs were designed and anchored with abundant boronic acid (BA) and photoreactive alkyl diazirine (Diaz) functional groups to obtain permanently tethered Fc-fused Siglec-2 and antiserum amyloid A (SAA) mAb with the assistance of reversible boronate affinity and UV light activation in an orientation-controlled manner. The Siglec-2-Fc-functionalized MNPs showed excellent stability in fetal bovine serum (FBS) and excellent efficiency in the extraction of cell membrane glycoproteins. The anti-SAA mAb-functionalized MNPs maintained active Ab orientation and preserved antigen recognition capability in biological samples. Thus, the BA-Diaz-based strategy holds promise for the immobilization of glycoproteins, such as antibodies, with the original protein binding activity maintained, which can provide better enrichment for the sensitive detection of target proteins.

One-Pot Two-Nanoprobe Assay Uncovers Targeted Glycoprotein Biosignature.

We report a one-pot two-nanoprobe approach coupled to mass spectrometry for simultaneous quantification and post-translational modification (PTM) profiling of targeted protein in biofluid. Using N-glycoprotein as model, the assay employs two nanoprobes, antibody-conjugated SiO2 nanoparticles and lectin-conjugated magnetic Fe3O4 nanoparticles, to achieve target glycoprotein isolation from biofluid and subsequent glycopeptide enrichment in a single tube. As demonstrated on α-fetoprotein (AFP), a serum biomarker for hepatocellular carcinoma (HCC), the assay has high purification specificity (20 glycopeptides) with 2-fold and 10-fold superior total glycopeptide intensity compared to non-one-pot method (9 glycopeptides) or without enrichment (6 glycopeptides), respectively. By multiple reaction monitoring mass spectrometry (MRM-MS) analysis of the nonglycopeptides, the assay can quantify low abundant AFP expression (0.5 ng) with good correlation with conventional ELISA method (Pearson's r = 0.987). Furthermore, we present the first study revealing AFP glycopeptide signatures of individual HCC patients, comprised of 23 heterogeneous glycoforms of bi- and triantennary, core and terminal fucosylation, and mono- to trisialylation. In addition to 12 novel AFP glycoforms, our quantification result uncovers five abundant glycoforms in HCC, including 3 core-fucosylated (CF) forms. These identified CF forms may be evaluated in future studies as potential targets in a glycopeptide biomarker panel to further improve accuracy of conventional AFP-L3 tests. Through this one-pot assay, a comprehensive target protein profile comprised of protein expression and glycosylation pattern was achieved in simple protocol with high sensitivity, reduced analysis time, and minute starting material. This assay can be extended to other PTM biosignatures by conjugation of other affinity ligands on the nanoprobe.

Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy.

Hepatocellular carcinoma (HCC), one of the most common causes of cancer-related deaths, carries a 5-year survival rate of 18%, underscoring the need for robust biomarkers. In spite of the increased availability of HCC related literatures, many of the promising biomarkers reported have not been validated for clinical use. To narrow down the wide range of possible biomarkers for further clinical validation, bioinformaticians need to sort them out using information provided in published works. Biomedical text mining is an automated way to obtain information of interest within the massive collection of biomedical knowledge, thus enabling extraction of data for biomarkers associated with certain diseases. This method can significantly reduce both the time and effort spent on studying important maladies such as liver diseases. Herein, we report a text mining-aided curation pipeline to identify potential biomarkers for liver cancer. The curation pipeline integrates PubMed E-Utilities to collect abstracts from PubMed and recognize several types of named entities by machine learning-based and pattern-based methods. Genes/proteins from evidential sentences were classified as candidate biomarkers using a convolutional neural network. Lastly, extracted biomarkers were ranked depending on several criteria, such as the frequency of keywords and articles and the journal impact factor, and then integrated into a meaningful list for bioinformaticians. Based on the developed pipeline, we constructed MarkerHub, which contains 2128 candidate biomarkers extracted from PubMed publications from 2008 to 2017. Database URL: http://markerhub.iis.sinica.edu.tw.

Monodispersity of magnetic immuno-nanoprobes enhances the detection sensitivity of low abundance biomarkers in one drop of serum.

To enhance the detection sensitivity of target clinical protein biomarkers, a simple and rapid nanoprobe-based immuno-affinity mass spectrometry assay employing biocompatible monodisperse magnetic nanoparticles (MNPs) is reported herein. The MNPs were synthesized via a streamlined protocol that includes (a) fabrication of core MNPs using the thermal decomposition method to minimize aggregation, (b) surface protection by gold coating (MNP@Au) and surfactant coating using MNP@IGEPAL to improve hydrophilicity, and lastly, (c) oriented functionalization of antibodies to maximize immuno-affinity. The enrichment performances of the monodisperse MNPs for the C-reactive protein (CRP) serum biomarker were then evaluated and compared with aggregated magnetic nanoparticles synthesized from the conventional co-precipitation method (MNP(CP)). The detection sensitivity for CRP at an extremely low amount of serum sample (1 µL) was enhanced ∼19- and ∼15-fold when monodisperse MNP@Au and MNP@IGEPAL, respectively, were used. Furthermore, the detection sensitivity of CRP by this approach (1 ng mL(-1), S/N = 3) provided a 1000-fold sensitivity enhancement to the clinical cut-off (1 µg mL(-1)) of CRP. We supposed that these observed improvements are due to the enhanced nanoparticle dispersibility and size uniformity which eliminated completely other non-specific binding of high-abundance serum proteins. Most interestingly, the enrichment efficiency correlates more closely with the MNP dispersibility than the ligand density. Our investigation revealed the critical role of MNP dispersibility, as well as provided mechanistic insight into its impact on immunoaffinity enrichment and detection of CRP in one drop of serum sample. This strategy offers an essential advantage over the other methods by providing a simple and facile biofunctionalization protocol while maintaining excellent solvent dispersibility of MNPs.

LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations.

Biomarkers are biomolecules in the human body that can indicate disease states and abnormal biological processes. Biomarkers are often used during clinical trials to identify patients with cancers. Although biomedical research related to biomarkers has increased over the years and substantial effort has been expended to obtain results in these studies, the specific results obtained often contain ambiguities, and the results might contradict each other. Therefore, the information gathered from these studies must be appropriately integrated and organized to facilitate experimentation on biomarkers. In this study, we used liver cancer as the target and developed a text-mining-based curation system named LiverCancerMarkerRIF, which allows users to retrieve biomarker-related narrations and curators to curate supporting evidence on liver cancer biomarkers directly while browsing PubMed. In contrast to most of the other curation tools that require curators to navigate away from PubMed and accommodate distinct user interfaces or Web sites to complete the curation process, our system provides a user-friendly method for accessing text-mining-aided information and a concise interface to assist curators while they remain at the PubMed Web site. Biomedical text-mining techniques are applied to automatically recognize biomedical concepts such as genes, microRNA, diseases and investigative technologies, which can be used to evaluate the potential of a certain gene as a biomarker. Through the participation in the BioCreative IV user-interactive task, we examined the feasibility of using this novel type of augmented browsing-based curation method, and collaborated with curators to curate biomarker evidential sentences related to liver cancer. The positive feedback received from curators indicates that the proposed method can be effectively used for curation. A publicly available online database containing all the aforementioned information has been constructed at http://btm.tmu.edu.tw/livercancermarkerrif in an attempt to facilitate biomarker-related studies. DATABASE URL: http://btm.tmu.edu.tw/LiverCancerMarkerRIF/

Ruthenium complexes of thiaporphyrin and dithiaporphyrin.

Successful synthesis and characterization of the six-coordinated complex [Ru(STTP)(CO)Cl] (1; STTP = 5,10,15,20-tetratolyl-21-thiaporphyrinato) allowed the development of the coordination chemistry of ruthenium-thiaporphyrin through dechlorination and metathesis reactions. Accordingly, [Ru(II)(STTP)(CO)X] (X = NO(3)(-) (2), NO(2)(-) (3), and N(3)(-) (4)) was synthesized and analyzed by single-crystal X-ray structural determination and NMR, UV-vis, and FT-IR spectroscopic methods. An independent reaction of STPPH and [Ru(COD)Cl(2)] led to [Ru(III)(STTP)Cl(2)] (5), which possessed a higher-valent Ru(III) center and exhibited good stability in the solution state. This stability allowed reversible redox processes in a cyclic voltammetric study. Reactions of [Ru(S(2)TTP)Cl(2)] (S(2)TTP = 5,10,15,20-tetratolyl-21,23-dithiaporphyrinato) with AgNO(3) and NaSePh, also via the metathesis strategy, resulted in novel dithiaporphyrin complexes [Ru(II)(S(2)TTP)(NO(3))(2)] (6) and [Ru(0)(S(2)TTP)(PhSeCH(2)SePh)(2)] (7), respectively. The structures of 6 and 7 were corroborated by X-ray crystallographic analyses. Complex 7 is an unprecedented ruthenium(0)-dithiaporphyrin with two bis(phenylseleno)methanes as axial ligands. A comparison of the analyses of the crude products from reactions of NaSePh and CH(2)Cl(2) with or without [Ru(S(2)TTP)Cl(2)], further supported by UV-vis spectral changes under stoichiometric reactions between [Ru(S(2)TTP)Cl(2)] and NaSePh, suggested a reaction sequence in the order of (1) formation of a putative [Ru(II)(S(2)TTP)(SePh)(2)] intermediate, followed by (2) the concerted formation of PhSe-CH(2)Cl and simultaneously a reduction of Ru(II) to Ru(0) and finally (3) nucleophilic substitution of PhSeCH(2)Cl by excess PhSe(-), resulting in PhSeCH(2)SePh, which readily coordinated to the Ru(0) and completed the formation of bis(phenylseleno)methane complex 7.

Factors that regulate the conformation of m-benziporphodimethene complexes: agostic metal-arene interaction, hydrogen bonding, and η2,π coordination.

Group 12 and silver(I) tetramethyl-m-benziporphodimethene (TMBPDM) complexes with phenyl, methylbenzoate, or nitrophenyl groups as meso substituents were synthesized and fully characterized. The dimeric silver(I) complex displays an unusual η(2),π coordination from the ß-pyrrolic C=C bond to the silver ion. All of the complexes displayed a close contact between the metal ion and the inner C(22)-H(22) on the m-phenylene ring. The downfield chemical shifts of H(22) and large coupling constants between Cd(II) and H(22) strongly support the presence of an agostic interaction between the metal ion and inner C(22)-H(22). Crystal structures revealed that the syn form is the predominant conformation for TMBPDM complexes. This is distinctively different from the exclusive anti conformation observed in m-benziporphyrin and tetraphenyl-m-benziporphodimethene (TPBPDM) complexes. Evidently, intramolecular hydrogen-bonding interactions between axial chloride and methyl groups stabilize syn conformations. Unlike the merely syn conformation observed in the solid-state structures of TMBPDM complexes that contain an axial chloride, in solution these complexes display highly solvent- and temperature-dependent syn/anti ratio changes. The observation of dynamic (1)H NMR spectroscopic scrambling between syn and anti conformations from the titration of chloride ion into the solution of the TMBPDM complex suggests that axial ligand exchange is a likely pathway for the conversion between syn and anti forms. Theoretical calculations revealed that intermolecular hydrogen-bonding interactions between the axial chloride and CHCl(3) stabilizes the anti conformation, which explains the increased ratio for the anti form when dichloromethane or chloroform was used as the solvent.