Boronic acid lectin affinity chromatography (BLAC). 2. Affinity micropartitioning-mediated comparative glycosylation profiling

As a continuation of our work on boronic acid lectin affinity chromatography (BLAC), in this paper we introduce an automated affinity micropartitioning approach using combined boronic acid and concanavalin A (BLAC/Con A) resin-filled micropipette tips to isolate and enrich human serum glycoproteins. The N-linked oligosaccharides of the partitioned glycoproteins were removed by PNGase F enzyme digestion, followed by 8-aminopyrene-1,3,6-trisulfonic acid labeling. Capillary gel electrophoresis with blue LED-induced fluorescence detection was applied in a multiplexed format for comparative glycan profiling. The efficiency of BLAC affinity micropartitioning was compared with that of the individual lectin and pseudolectin affinity enrichment. Finally, we report on our findings in glycosylation differences in human serum samples from healthy and prostate cancer patients by applying BLAC/Con A micropipette tip-based enrichment and comparative multicapillary gel electrophoresis analysis of the released and labeled glycans.     

Imaging Glycosylation In Vivo by Metabolic Labeling and Magnetic Resonance Imaging

Glycosylation is a ubiquitous post‐translational modification, present in over 50 % of the proteins in the human genome, 1 with important roles in cell–cell communication and migration. Interest in glycome profiling has increased with the realization that glycans can be used as biomarkers of many diseases, 2 including cancer. 3 We report here the first tomographic imaging of glycosylated tissues in live mice by using metabolic labeling and a gadolinium‐based bioorthogonal MRI probe. Significant N‐azidoacetylgalactosamine dependent T₁ contrast was observed in vivo two hours after probe administration. Tumor, kidney, and liver showed significant contrast, and several other tissues, including the pancreas, spleen, heart, and intestines, showed a very high contrast (>10‐fold). This approach has the potential to enable the rapid and non‐invasive magnetic resonance imaging of glycosylated tissues in vivo in preclinical models of disease.     

Boronic Acid Functionalized Core–Satellite Composite Nanoparticles for Advanced Enrichment of Glycopeptides and Glycoproteins

A core–satellite‐structured composite material has been successfully synthesized for capturing glycosylated peptides or proteins. This novel hybrid material is composed of a silica‐coated ferrite “core” and numerous “satellites” of gold nanoparticles with lots of “anchors”. The anchor, 3‐aminophenylboronic acid, designed for capturing target molecules, is highly specific toward glycosylated species. The long organic chains bridging the gold surface and the anchors could reduce the steric hindrance among the bound molecules and suppress nonspecific bindings. Due to the excellent structure of the current material, the trap‐and‐release enrichment of glycosylated samples is quite simple, specific, and effective. Indeed, the composite nanoparticles could be used for enriching glycosylated peptides and proteins with very low concentrations, and the enriched samples can be easily separated from bulk solution by a magnet. By using this strategy, the recovery of glycopeptides and glycoproteins after enrichment were found to be 85.9 and 71.6 % separately, whereas the adsorption capacity of the composite nanoparticles was proven to be more than 79 mg of glycoproteins per gram of the material. Moreover, the new composite nanoparticles were applied to enrich glycosylated proteins from human colorectal cancer tissues for identification of N‐glycosylation sites. In all, 194 unique glycosylation sites mapped to 155 different glycoproteins have been identified, of which 165 sites (85.1 %) were newly identified.     

The use of matrix coating assisted by an electric field (MCAEF) to enhance mass spectrometric imaging of human prostate cancer biomarkers

In this work, we combined a newly developed matrix coating technique – matrix coating assisted by an electric field (MCAEF) and matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) to enhance the imaging of peptides and proteins in tissue specimens of human prostate cancer. MCAEF increased the signal‐to‐noise ratios of the detected proteins by a factor of 2 to 5, and 232 signals were detected within the m/z 3500–37500 mass range on a time‐of‐flight mass spectrometer and with the sinapinic acid MALDI matrix. Among these species, three proteins (S100‐A9, S100‐A10, and S100‐A12) were only observed in the cancerous cell region and 14 proteins, including a fragment of mitogen‐activated protein kinase/extracellular signal‐regulated kinase kinase kinase 2, a fragment of cAMP‐regulated phosphoprotein 19, 3 apolipoproteins (C‐I, A‐I, and A‐II), 2 S100 proteins (A6 and A8), β‐microseminoprotein, tumor protein D52, α‐1‐acid glycoprotein 1, heat shock protein β‐1, prostate‐specific antigen, and 2 unidentified large peptides at m/z 5002.2 and 6704.2, showed significantly differential distributions at the p < 0.05 (t‐test) level between the cancerous and the noncancerous regions of the tissue. Among these 17 species, the distributions of apolipoprotein C‐I, S100‐A6, and S100‐A8 were verified by immunohistological staining. In summary, this study resulted in the imaging of the largest group of proteins in prostate cancer tissues by MALDI‐MS reported thus far, and is the first to show a correlation between S100 proteins and prostate cancer in a MS imaging study. The successful imaging of the three proteins only found in the cancerous tissues, as well as those showing differential expressions demonstrated the potential of MCAEF‐MALDI/MS for the in situ detection of potential cancer biomarkers. Copyright © 2015 John Wiley & Sons, Ltd.     

Cell surface glycoprotein profiling of cancer cells based on bioorthogonal chemistry

Bioorthogonal chemistry refers to chemical reactions that can occur within a living system without altering native biochemical processes. Applications of this concept extend to studies on a group of biomolecules that includes glycans, proteins, and lipids. In this study, a strategy for isolating cell surface glycoproteins and based on bioorthogonal chemistry was employed to identify new cancer-related glycoproteins. A novel alkyne reagent containing one disulfide bond was synthesized for the enrichment of glycoproteins metabolized with peracetylated N-azidoacetylmannosamine, which was applied on three different cancer cell lines, and all isolated proteins were analyzed by high-performance liquid chromatography-tandem mass spectrometry. The strategy of purifying cell surface glycoproteins introduced in this article was shown to be reliable, and a total of 56 cell surface glycoproteins were identified. Neuronal cell adhesion molecule was found uniquely expressed in A549 lung adenocarcinoma, and its expression in non-small-cell lung carcinomas was detected by immunohistochemistry. Furthermore, a significant increase of neuronal cell adhesion molecule expression was identified in non-small-cell lung adenocarcinoma compared with adjacent noncancerous tissues, and could be a novel potential target and marker in cancer treatment and detection.     

Systematic and site-specific analysis of N-sialoglycosylated proteins on the cell surface by integrating click chemistry and MS-based proteomics

Glycoproteins on the cell surface are ubiquitous and essential for cells to interact with the extracellular matrix, communicate with other cells, and respond to environmental cues. Although surface sialoglycoproteins can dramatically impact cell properties and represent different cellular statuses, global and site-specific analysis of sialoglycoproteins only on the cell surface is extraordinarily challenging. An effective method integrating metabolic labeling, copper-free click chemistry and mass spectrometry-based proteomics was developed to globally and site-specifically analyze surface N-sialoglycoproteins. Surface sialoglycoproteins metabolically labeled with a functional group were specifically tagged through copper-free click chemistry, which is ideal because it is quick, specific and occurs under physiological conditions. Sequentially tagged sialoglycoproteins were enriched for site-specific identification by mass spectrometry. Systematic and quantitative analysis of the surface N-sialoglycoproteome in cancer cells with distinctive invasiveness demonstrated many N-sialoglycoproteins up-regulated in invasive cells, the majority of which contained cell adhesion-related domains. This method is very effective to globally and site-specifically analyze N-sialoglycoproteins on the cell surface, and will have extensive applications in the biological and biomedical research communities. Site-specific information regarding surface sialoglycoproteins can serve as biomarkers for disease detection, targets for vaccine development and drug treatment.     

Boronic acid functionalized Fe3O4 magnetic microspheres for the specific enrichment of glycoproteins

Glycoproteins are useful biomarkers and therapeutic targets for a number of diseases, including infections and cancer. However, identification and isolation of low‐abundant glycoproteins remains a significant challenge that limits their application. Thus, methods of specific and selective glycoprotein enrichment are required. In this study, novel phenylboronic acid functionalized magnetic microspheres were successfully synthesized. Fe₃O₄ microspheres were synthesized by using a hydrothermal method and were coated with tetraethyl orthosilicate using an ultrasonic method to form a core‐shell structure. Compared to the conventional mechanical stirring for 12 h, the ultrasonic method saved about 7 h in processing time, and the home‐made magnetic microspheres had better dispersibility and homogeneity. Subsequently, the magnetic microspheres were modified by addition of an amino group and a carboxyl group, in sequence. Finally, 3‐aminophenylboronic acid, as the functional monomer, was linked to the magnetic microspheres for capturing glycoprotein/glycopeptides. The results of this study indicate that phenylboronic acid functionalized magnetic microspheres show excellent adsorption performance toward glycoprotein/glycopeptides. The maximum absorbing capacity of the microspheres for fetuin was 108 mg/g, and the enrichment efficiency reached 89.7%, indicating their potential to separate and enrich glycoproteins from the complex biological samples.     

Terminal Alkenes as Versatile Chemical Reporter Groups for Metabolic Oligosaccharide Engineering

The Diels–Alder reaction with inverse electron demand (DAinv reaction) of 1,2,4,5‐tetrazines with electron rich or strained alkenes was proven to be a bioorthogonal ligation reaction that proceeds fast and with high yields. An important application of the DAinv reaction is metabolic oligosaccharide engineering (MOE) which allows the visualization of glycoconjugates in living cells. In this approach, a sugar derivative bearing a chemical reporter group is metabolically incorporated into cellular glycoconjugates and subsequently derivatized with a probe by means of a bioorthogonal ligation reaction. Here, we investigated a series of new mannosamine and glucosamine derivatives with carbamate‐linked side chains of varying length terminated by alkene groups and their suitability for labeling cell‐surface glycans. Kinetic investigations showed that the reactivity of the alkenes in DAinv reactions increases with growing chain length. When applied to MOE, one of the compounds, peracetylated N‐butenyloxycarbonylmannosamine, was especially well suited for labeling cell‐surface glycans. Obviously, the length of its side chain represents the optimal balance between incorporation efficiency and speed of the labeling reaction. Sialidase treatment of the cells before the bioorthogonal labeling reaction showed that this sugar derivative is attached to the glycans in form of the corresponding sialic acid derivative and not epimerized to another hexosamine derivative to a considerable extent.     

Activity‐Based Probes for 15‐Lipoxygenase‐1

Human 15‐lipoxygenase‐1 (15‐LOX‐1) plays an important role in several inflammatory lung diseases, such as asthma, COPD, and chronic bronchitis, as well as various CNS diseases, such as Alzheimer's disease, Parkinson's disease, and stroke. Activity‐based probes of 15‐LOX‐1 are required to explore the role of this enzyme further and to enable drug discovery. In this study, we developed a 15‐LOX‐1 activity‐based probe for the efficient activity‐based labeling of recombinant 15‐LOX‐1. 15‐LOX‐1‐dependent labeling in cell lysates and tissue samples was also possible. To mimic the natural substrate of the enzyme, we designed activity‐based probes that covalently bind to the active enzyme and include a terminal alkene as a chemical reporter for the bioorthogonal linkage of a detectable functionality through an oxidative Heck reaction. The activity‐based labeling of 15‐LOX‐1 should enable the investigation and identification of this enzyme in complex biological samples, thus opening up completely new opportunities for drug discovery.     

Direct Visualization of Live Zebrafish Glycans via Single‐Step Metabolic Labeling with Fluorophore‐Tagged Nucleotide Sugars

Dynamic turnover of cell‐surface glycans is involved in a myriad of biological events, making this process an attractive target for in vivo molecular imaging. Metabolic glycan labeling coupled with bioorthogonal chemistry has paved the way for visualizing glycans in living organisms. However, a two‐step labeling sequence is required, which suffers from the tissue‐penetration difficulties of the imaging probes. Here, by exploring the substrate promiscuity of endogenous glycosyltransferases, we developed a single‐step fluorescent glycan labeling strategy by using fluorophore‐tagged analogues of the nucleotide sugars. Injecting fluorophore‐tagged sialic acid and fucose into the yolk of zebrafish embryos at the one‐cell stage enables systematic imaging of sialylation and fucosylation in live zebrafish embryos at distinct developmental stages. From these studies, we obtained insights into the role of sialylated and fucosylated glycans in zebrafish hematopoiesis.     

Effect of temperature on surface properties of cervical tissue homogenate and organic phase monolayers

The temperature dependence of Langmuir monolayers of normal and cancerous human cervical tissues and their organic phases between temperatures of 37 and 45 degrees C was evaluated. Analysis of the surface pressure-area isotherms revealed significantly different increase in fluidity of the cancerous cervical tissue monolayer at 42 degrees C as opposed to the normal cervical tissue monolayers (p<0.05). Similarly, in the case of cervical cancerous organic phase monolayers significant increase of fluidity was observed at 40 degrees C whereas no such change was observed in the normal cervical organic phase monolayers. The effect of temperature was found to be different in cancerous and normal cervical tissues and this may be due to the different lipid profiles in them. Cancerous cervical tissues had 1.8-fold higher total lipids as compared to the normals. Similarly, the PC, PE, PI, PG, SM and PS levels in cancerous cervical tissues were 3.6, 2.0, 2.3, 4.7, 1.7 and 2.2 times higher than those of normal cervical tissues, respectively. Significant cancer-normal difference in minimum surface tension and hysteresis area was found at all temperatures studied for both tissue homogenates and organic phases. For example, cancerous tissue homogenates showed minimum surface tensions of 51.9+/-4.6, 54.4+/-5.9, 57.6+/-6.0 and 51.9+/-5.6mN/m at temperatures 37, 40, 42 and 45 degrees C whereas the corresponding values for normal cervical tissue homogenates were 39.3+/-3.6, 39.2+/-3.7, 39.2+/-3.8 and 39.1+/-3.6, respectively. The fluidity change at hyperthermic range of temperature can be correlated to the increased efficiency of drug on combination therapy with hyperthermia. These results may have implications in manipulating the fluidity of cervical cancer tissue membranes for better permeability thereby leading to better therapeutic strategies for cervical cancer.     

Structural Elucidation of the Bispecificity of A Domains as a Basis for Activating Non‐natural Amino Acids

Many biologically active peptide secondary metabolites of bacteria are produced by modular enzyme complexes, the non‐ribosomal peptide synthetases. Substrate selection occurs through an adenylation (A) domain, which activates the cognate amino acid with high fidelity. The recently discovered A domain of an Anabaenopeptin synthetase from Planktothrix agardhii (ApnA A₁) is capable of activating two chemically distinct amino acids (Arg and Tyr). Crystal structures of the A domain reveal how both substrates fit into to binding pocket of the enzyme. Analysis of the binding pocket led to the identification of three residues that are critical for substrate recognition. Systematic mutagenesis of these residues created A domains that were monospecific, or changed the substrate specificity to tryptophan. The non‐natural amino acid 4‐azidophenylalanine is also efficiently activated by a mutant A domain, thus enabling the production of diversified non‐ribosomal peptides for bioorthogonal labeling.     

Reversible Lysine Modification on Proteins by Using Functionalized Boronic Acids

Iminoboronates have been utilized to successfully install azide and alkyne bioorthogonal functions on proteins, which may then be further reacted with their bioorthogonal counterparts. These constructs were also used to add polyethylene glycol (PEG) to insulin, a modification which has been shown to be reversible in the presence of fructose. Finally, iminoboronates were used to assemble a folic acid/paclitaxel small‐molecule/drug conjugate in situ with an IC₅₀ value of 20.7 nM against NCI‐H460 cancer cells and negligible cytotoxicity against the CRL‐1502 noncancer cells.     

Analysis of fatty acids in lung tissues using gas chromatography-mass spectrometry preceded by derivatization-solid-phase microextraction with a novel fiber

In this article, a laboratory-made sol-gel derived fiber with butyl methacrylate/hydroxy-terminated silicone oil (BMA/OH-TSO) coating was first used for headspace solid-phase microextraction (HS-SPME) of medium and long chain fatty acids after derivatization and applied to the analysis of fatty acids in lung tissues by coupling to gas chromatography-mass spectrometry (GC-MS). The experimental parameters for derivatization, HS-SPME and desorption were optimized. Fatty acids in cancerous lung tissues from five patients with lung cancer were determined under the optimized conditions. Normal lung tissues from the same five patients were used as controls. This fiber showed higher extraction efficiency for fatty acids after derivatization when compared with commercial polydimethylsiloxane (PDMS) and polydimethylsiloxane-divinylbenzene (PDMS/DVB) fibers due to the three-dimensional network in the coating. The method presented in this paper showed satisfactory precision, accuracy, linearity and limits of detection (LODs). The relative standard deviation values were below 13.3% (n = 5) and the recoveries obtained ranged from 76.35% to 107.0%. The results obtained using the SPME method were also compared with those got by using liquid-liquid extraction (LLE) technique. It was found that the sensitivity could be enhanced by the SPME method. The analysis of the cancerous lung tissues and normal controls from five patients with lung cancer indicated that the main components of lung tissue were palmitic acid (C_16:0), stearic acid (C_18:0) and lignoceric acid (C_24:0). A comparison between the levels of the fatty acids in cancerous lung tissues and normal controls from the same a patient with lung cancer shows that most of the saturated fatty acids showed higher levels in cancerous lung tissues, while unsaturated fatty acids showed higher levels in normal controls on the whole.     

Boronic Acids as Bioorthogonal Probes for Site‐Selective Labeling of Proteins

Over the past two decades, bioorthogonal chemistry has become a preferred tool to achieve site‐selective modifications of proteins. However, there are only a handful of commonly applied bioorthogonal reactions and they display some limitations, such as slow rates, use of unstable or cytotoxic reagents, and side reactions. Hence, there is significant interest in expanding the bioorthogonal chemistry toolbox. In this regard, boronic acids have recently been introduced in bioorthogonal chemistry and are exploited in three different strategies: 1) boronic ester formation between a boronic acid and a 1,2‐cis diol; 2) iminoboronate formation between 2‐acetyl/formyl‐arylboronic acids and hydrazine/hydroxylamine/semicarbazide derivatives; 3) use of boronic acids as transient groups in a Suzuki–Miyaura cross‐coupling or other reactions that leave the boronyl group off the conjugation product. In this Review, we summarize progress made in the use of boronic acids in bioorthogonal chemistry to enable site‐selective labeling of proteins and compare these methods with the most commonly utilized bioorthogonal reactions.     

Affinity‐Labeling‐Based Introduction of a Reactive Handle for Natural Protein Modification

A new chemical method to site‐specifically modify natural proteins without the need for genetic manipulation is described. Our strategy involves the affinity‐labeling‐based attachment of a unique reactive handle at the surface of the target protein, and the subsequent selective transformation of the reactive handle by a bioorthogonal reaction to introduce a variety of functional probes into the protein. To demonstrate this approach, we synthesized labeling reagents that contain: 1) a benzenesulfonamide ligand that directs specifically to bovine carbonic anhydrase II (bCA), 2) an electrophilic epoxide group for protein labeling, 3) an exchangeable hydrazone bond linking the ligand and the epoxide group, and 4) an iodophenyl or acetylene handle. By incubating the labeling reagent with bCA, the reactive handle was covalently attached at the surface of bCA through epoxide ring opening. Either after or before removing the ligand by a hydrazone/oxime‐exhange reaction, which restores the enzymatic activity, the reactive handle incorporated could be derivatized by Suzuki coupling or Huisgen cycloaddition reactions. This method is also applicable to the target‐specific multiple modification in a protein mixture. The availability of various (photo)affinity‐labeling reagents and bioorthogonal reactions should extend the flexibility of this strategy for the site‐selective incorporation of many functional molecules into proteins.     

Direct identification of proteins from T47D cells and murine brain tissue by matrix-assisted laser desorption/ionization post-source decay/collision-induced dissociation

The purpose of this study is to determine the feasibility of the direct matrix-assisted laser desorption/ionization (MALDI) identification of proteins in fixed T47D breast cancer cells and murine brain tissues. The ability to identify proteins from cells and tissue may lead to biomarkers that effectively predict the onset of defined disease states, and their dynamic behavior could be an important hint for drug target discoveries. Direct tissue application of trypsin allows protein identification in cells and tissues, while maintaining spatial integrity and intracellular organization. Using a chemical printer, matrix was co-registered on trypsinized human T47D breast cancer cells and cryo-preserved sections of murine brain tissue, followed by MALDI post-source decay (PSD) or MALDI collision-induced dissociation (CID), respectively. Mass-to-charge (m/z) data from the cells and brain tissues were processed using Mascot software interrogation of the National Center for Biotechnology Information (NCBI) database. Histone H2B was identified from cultured T47D human breast cancer cells. Tubulin beta2 was identified from mouse brain cortex following an induced stroke. These results suggest that MALDI PSD/CID, combined with bioinformatics, can be used for the direct identification of proteins from cells and tissues. Refinements in preparation techniques may improve this approach to provide a tool for quantitative proteomics and clinical analysis.     

Unequivocal resolution of multiplets in MR spectra for prostate cancer diagnostics achieved by the fast Padé transform

We perform mathematical modeling with the fast Padé transform (FPT) according to magnetic resonance (MR)-time signals as encoded in vitro from normal glandular and stromal prostate tissue and from prostate cancer. This is one of the most demanding signal processing problems in MR spectroscopy due to the abundance of diagnostically important multiplets (notably doublet and triplet resonances). The FPT provided exact reconstruction at short acquisition times (i.e. using only a fraction of the full signal length) of all the input spectral parameters for the data corresponding to prostate cancer and to normal glandular as well as stromal prostate tissue. This was achieved without any fitting or numerical integration of peak areas. The converged parametric results remained stable at longer partial signal lengths, including the case using the full signal length. The Padé absorption component spectra yielded unequivocal resolution of all the extracted physical resonances, including multiplet resonances and closely overlapping peaks of different metabolites. The capacity of the FPT to resolve and precisely quantify the physical resonances as encountered in normal tissue from two distinct regions of the prostate, as well as in prostate cancer is demonstrated. The spectra from prostate tissues are dense, which suggests that there is a rich array of metabolic information to be gleaned. The FPT is hereby shown to be optimally suited to retrieve that information. The FPT reliably yields the metabolite concentrations that could be of critical importance for distinguishing non-malignant from cancerous prostate tissue. Padé-optimized MRS could clearly aid prostate cancer diagnostics. This line of investigation will continue with experimentally encoded data from normal, hypertrophic and cancerous prostate tissue, in vitro and in vivo. We anticipate that Padé-optimized MRS will improve the specificity as well as sensitivity of MR-based modalities with respect to prostate cancer. This could have an important impact upon timely and accurate diagnosis of this malignancy, as well as aiding decision-making for therapeutic dilemmas.     

Chemiluminescent Probe for the In Vitro and In Vivo Imaging of Cancers Over‐Expressing NQO1

Activatable (turn‐on) probes that permit the rapid, sensitive, selective, and accurate identification of cancer‐associated biomarkers can help drive advances in cancer research. Herein, a NAD(P)H:quinone oxidoreductase‐1 (NQO1)‐specific chemiluminescent probe 1 is reported that allows the differentiation between cancer subtypes. Probe 1 incorporates an NQO1‐specific trimethyl‐locked quinone trigger moiety covalently tethered to a phenoxy‐dioxetane moiety through a para‐aminobenzyl alcohol linker. Bio‐reduction of the quinone to the corresponding hydroquinone results in a chemiluminescent signal. As inferred from a combination of in vitro cell culture analyses and in vivo mice studies, the probe is safe, cell permeable, and capable of producing a “turn‐on” luminescence response in an NQO1‐positive A549 lung cancer model. On this basis, probe 1 can be used to identify cancerous cells and tissues characterized by elevated NQO1 levels.     

Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics

The advances in bioorthogonal ligation methods have provided new opportunities for proteomic analysis of newly synthesized proteins, posttranslational modifications, and specific enzyme families using azide/alkyne-functionalized chemical reporters and activity-based probes. Efficient enrichment and elution of azide/alkyne-labeled proteins with selectively cleavable affinity tags are essential for protein identification and quantification applications. Here, we report the synthesis and comparative analysis of Na?S?O?-cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics. We demonstrated that ortho-hydroxyl substituent is required for efficient azobenzene-bond cleavage and show that these cleavable affinity tags can be used to identify newly synthesized proteins in bacteria targeted by amino acid chemical reporters as well as their sites of modification on endogenously expressed proteins. The azobenzene-based affinity tags are compatible with in-gel, in-solution, and on-bead enrichment strategies and should afford useful tools for diverse bioorthogonal proteomic applications.