Changes in the Proteome of Langat-Infected Ixodes scapularis ISE6 Cells: Metabolic Pathways Associated with Flavivirus Infection.

BACKGROUND: Ticks (Family Ixodidae) transmit a variety of disease causing agents to humans and animals. The tick-borne flaviviruses (TBFs; family Flaviviridae) are a complex of viruses, many of which cause encephalitis and hemorrhagic fever, and represent global threats to human health and biosecurity. Pathogenesis has been well studied in human and animal disease models. Equivalent analyses of tick-flavivirus interactions are limited and represent an area of study that could reveal novel approaches for TBF control. METHODOLOGY/PRINCIPAL FINDINGS: High resolution LC-MS/MS was used to analyze the proteome of Ixodes scapularis (Lyme disease tick) embryonic ISE6 cells following infection with Langat virus (LGTV) and identify proteins associated with viral infection and replication. Maximal LGTV infection of cells and determination of peak release of infectious virus, was observed at 36 hours post infection (hpi). Proteins were extracted from ISE6 cells treated with LGTV and non-infectious (UV inactivated) LGTV at 36 hpi and analyzed by mass spectrometry. The Omics Discovery Pipeline (ODP) identified thousands of MS peaks. Protein homology searches against the I. scapularis IscaW1 genome assembly identified a total of 486 proteins that were subsequently assigned to putative functional pathways using searches against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. 266 proteins were differentially expressed following LGTV infection relative to non-infected (mock) cells. Of these, 68 proteins exhibited increased expression and 198 proteins had decreased expression. The majority of the former were classified in the KEGG pathways: "translation", "amino acid metabolism", and "protein folding/sorting/degradation". Finally, Trichostatin A and Oligomycin A increased and decreased LGTV replication in vitro in ISE6 cells, respectively. CONCLUSIONS/SIGNIFICANCE: Proteomic analyses revealed ISE6 proteins that were differentially expressed at the peak of LGTV replication. Proteins with increased expression following infection were associated with cellular metabolic pathways and glutaminolysis. In vitro assays using small molecules implicate malate dehydrogenase (MDH2), the citrate cycle, cellular acetylation, and electron transport chain processes in viral replication. Proteins were identified that may be required for TBF infection of ISE6 cells. These proteins are candidates for functional studies and targets for the development of transmission-blocking vaccines and drugs.

Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers.

We used a lectin chromatography/MS-based approach to screen conditioned medium from a panel of luminal (less aggressive) and triple negative (more aggressive) breast cancer cell lines (n=5/subtype). The samples were fractionated using the lectins Aleuria aurantia (AAL) and Sambucus nigra agglutinin (SNA), which recognize fucose and sialic acid, respectively. The bound fractions were enzymatically N-deglycosylated and analyzed by LC-MS/MS. In total, we identified 533 glycoproteins, ∼90% of which were components of the cell surface or extracellular matrix. We observed 1011 glycosites, 100 of which were solely detected in ≥3 triple negative lines. Statistical analyses suggested that a number of these glycosites were triple negative-specific and thus potential biomarkers for this tumor subtype. An analysis of RNaseq data revealed that approximately half of the mRNAs encoding the protein scaffolds that carried potential biomarker glycosites were up-regulated in triple negative vs luminal cell lines, and that a number of genes encoding fucosyl- or sialyltransferases were differentially expressed between the two subtypes, suggesting that alterations in glycosylation may also drive candidate identification. Notably, the glycoproteins from which these putative biomarker candidates were derived are involved in cancer-related processes. Thus, they may represent novel therapeutic targets for this aggressive tumor subtype.

Enrichment of cysteine-containing peptides from tryptic digests using a quaternary amine tag.

A new strategy for specifically targeting cysteine-containing peptides in a tryptic digest is described. The method is based on quantitatively derivatizing cysteine residues with a quaternary amine tag (QAT). Tags were introduced into proteins following reduction of disulfide bonds through derivatization of cysteine residues with (3-acrylamidopropyl)trimethylammonium chloride. After trypsin digestion, derivatized cysteine-containing peptides were enriched by strong cation exchange chromatography. The method was validated using model peptides and a protein. The QAT strategy has several advantages over other methods for the selection of cysteine-containing peptides. One is that it increases the ionization efficiency of cysteine-containing peptides. The other is that chromatographic selection is achieved with simple, robust cation exchange chromatography columns. As a result, this new strategy provides a simple way to facilitate enrichment of cysteine-containing peptides, thereby reducing sample complexity in bottom-up proteomics.

Contributions of commercial sorbents to the selectivity in immobilized metal affinity chromatography with Cu(II).

Immobilized copper(II) affinity chromatography [Cu(II)-immobilized metal affinity chromatography (IMAC)] has been used in proteomics to simplify sample mixtures by selecting histidine-containing peptides from proteolytic digests. This paper examines the specificity of four different support materials with an iminodiacetic acid (IDA) stationary phase in the selection of only histidine-containing peptides in the single step capture-release mode. Three of the sorbents examined were commercially available: HiTrap Chelating HP (agarose), TSK Chelate-5PW, and Poros 20MC. IDA was also immobilized on CIM discs (monolithic glycidylmethacrylate-ethylene dimethacrylate). Tryptic digests of transferrin and beta-galactosidase were used as model samples to evaluate these sorbents. It was found that among the examined matrices, the TSK Chelate-5PW sorbent bound histidine-containing peptides the strongest, while Poros matrix was found to have a high degree of non-specific bindings. Agarose-based columns showed relatively high selectivity and specificity.

High-speed label-free detection by spinning-disk micro-interferometry.

Spinning-disk interferometers are a new class of analytic sensors to detect immobilized biomolecules with high speed and high sensitivity. The disks are composed of a large number of surface-normal self-referencing interferometers, analogous to an optical CD, but operating on the principle of microdiffraction quadrature that achieves sensitive linear detection of bound molecules. The surface-normal structures have a small footprint of only 20 microm each, allowing potential integration to over a million interferometric elements per disk. We have fabricated interferometric microstructures on silicon and on dielectric mirror disks to demonstrate the basic principles of the BioCD. We have detected the presence of immobilized anti-mouse IgG and the specific binding of 10 femtomol of mouse IgG at a sampling rate of 100 kilo-samples/s, while also demonstrating negligible non-specific binding. This technique provides a label-free method that could potentially screen hundreds to thousands of proteins per disk.

Structural characterization of plasmenylcholine photooxidation products.

Oxidative damage to plasmenyl-type lipids contributes to decreased membrane barrier function, loss of membrane structure and formation of nonlamellar defects in membrane bilayers. Previous results from this laboratory have shown that membrane-soluble sensitizers (e.g. zinc phthalocyanine and bacteriochlorophyll a) mediate the photooxidation of palmitoyl plasmenylcholine (1-O-alk-1'-Z-enyl-2-palmitoyl-sn-glycero-3-phosphocholine; PPlsC) vesicles with the subsequent creation of lamellar defect structures, vesicle contents leakage and membrane-membrane fusion. Because plasmalogen lipids are significant components of sarcoplasma and myelin membranes, we sought to characterize the products of their photooxidation. This study focuses on the photooxidation of PPlsC vesicles in the presence of the water-soluble sensitizer, aluminum phthalocyanine tetrasulfonate (AlPcS4(4-)). Attack of photogenerated singlet oxygen on the 1-O-alkenyl ether linkage of PPlsC lipids was expected to generate dioxetane- and ene-type photoproducts. The products formed during continuous aerobic irradiation (28 mW/cm2, (610 nm) of PPlsC vesicles in the presence of AlPcS4(4-) were separated via reverse-phase high-performance liquid chromatography (HPLC) with electrochemical detection (ECD) or evaporative light-scattering detection (ELSD). Photooxidized dipalmitoyl-phosphatidylcholine-cholesterol vesicles (control) were used to optimize the HPLC-ECD conditions, using 7 alpha-hydroperoxy-cholesterol as standard. HPLC-ECD was found to be most sensitive for PPlsC hydroperoxides, whereas HPLC-ELSD was more sensitive for nonhydroperoxide photoproducts. The three major photoproducts formed during vesicle irradiation were isolated via preparative HPLC and then characterized by 1H-nuclear magnetic resonance and mass spectrometry. 1-Formyl-2-palmitoyl-sn-glycero-3-phosphocholine and 1-hydroxy-2-palmitoyl-sn-glycero-3-phosphocholine were identified as dioxetane cleavage products that coeluted at approximately 3 min. The second fraction (retention time [RT] = 48 min) was identified as a PPlsC allylic hydroperoxide. The third photoproduct, eluting at RT = 64 min, is tentatively identified as an oxidation product arising from allylic hydroperoxide degradation via Hock rearrangement or free radical decomposition.