High-resolution Fourier Transform Mass Spectrometry Research Articles

Abstract PO1-26-04: Patient-derived organotypic tissue cultures for organoid isolation and probing unique metabolic features of individual breast cancer patients

Abstract Patient-derived organotypic tissue cultures (PD-OTC) are unique models for probing how individual patient’s tumor microenvironment (TME) influences cancer development and treatment responses. They retain the patient tumor architecture and TME, that are difficult to recapitulate in other models, while affording flexible treatment options and comparison of cancer (CA) versus matched non-cancer (NC) tissue responses to treatments. We have developed a culturing method for establishing PD-OTC of breast cancer patients that exhibit CA tissue growth and extensive metabolic reprogramming between CA versus matched NC tissues while enabling patient-derived organoids (PDO) and fibroblasts to be isolated. Pairs of CA and NC tissues freshly resected from six patients bearing early-stage estrogen receptor/progesterone receptor positive ductal carcinoma were sliced at 750 µm, embedded in Matrigel, and cultured in a 6-well plate with a Biopore membrane insert and custom medium at 37°C/5% CO2 with gentle rocking (16-40 mg wet weight; n=3). Excess tissue slices were cryopreserved and kept at -196 °C. Culture media were sampled periodically for metabolite analysis by NMR. Microscopic examination revealed significant tissue, organoid-like, and fibroblast outgrowth after 1-1.5 month of culturing. Two to three days prior to the harvest of two patients’ (CZ16 and 17) OTC, the culture medium was replaced with [U-2H]-glucose + [U-13C,15N]-glutamine-containing medium to allow the two stable isotope tracers to be metabolized, followed by Stable Isotope-Resolved Metabolomic (SIRM) analysis by NMR and ion chromatography coupled with ultra high-resolution Fourier transform mass spectrometry (IC-UHRFTMS). Two separate pieces of the OTC were cut and each was assayed for glucose uptake and mitochondrial membrane potential by live fluorescence spectroscopy via a portable custom-built fluorescence microscope, and by histochemical analysis. Histological analysis showed that both CA and NC OTC of all patients maintained their structural integrity. SIRM analysis of two patients’ OTC revealed active catabolic and anabolic metabolism including glucose uptake/glycolysis, the Krebs cycle/mitochondrial membrane potential, the pentose phosphate pathway (PPP), gluconeogenesis, glycogen synthesis, and purine/pyrimidine/sugar nucleotides synthesis. The CA OTC of both patients showed enhanced glucose uptake, glycolysis, mitochondrial membrane potential/Krebs cycle, PPP, glycogen synthesis, and purine nucleotide synthesis, when compared with the matched NC OTC. Treatment-naïve CA OTC of CZ16 showed much more significant metabolic reprogramming (NAD+ metabolism, in particular) than CA OTC of CZ17 who has undergone neoadjuvant treatment, chemotherapy, and hormone therapy prior to surgery. Distinct metabolic features of breast CA tissues can be exploited as therapeutic targets. Organoids and fibroblasts were isolated from CA and/or NC OTC cultures and their characterization is in progress. When revived, cryopreserved OTC exhibited active metabolism and tissue/organoid/fibroblast outgrowth similarly to fresh OTC. In conclusion, our culturing method enables PD-OTC models to be established efficiently for early-stage breast cancer patients for downstream functional studies including live cell imaging and SIRM analysis. Organoids and fibroblasts can also be derived from < 20 mg of tissues for further studies. Future direction includes therapeutic studies on these patient-derived models to better understand and predict individual patient’s responses to therapy. Citation Format: Teresa Fan, Carlos Goncalves, Jing Yan, Jahid Islam, Penghui Lin, Mohamed Kaddah, Richard Higashi, Andrew Lane, Caigang Zhu. Patient-derived organotypic tissue cultures for organoid isolation and probing unique metabolic features of individual breast cancer patients [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-26-04.

Isomeric fluorescence sensors for wide range detection of ionizing radiations

In order to achieve a wider range of ionizing radiations detection, novel fluorescence sensing materials have been developed that utilize the fluorescence enhancement phenomenon caused by the intramolecular photoinduced electron transfer (PET) effect. Two perylene diimide isomers PDI-P and PDI-B were designed and synthesized, and their molecular structures were characterized by high-resolution Fourier transform mass spectrometry (HRMS), nuclear magnetic resonance hydrogen and carbon spectroscopy (1H and 13C NMR). The interaction between ionizing radiation and fluorescent molecules was simulated by HCl titration. The results show that combining PDIs and HCl can improve fluorescence through the retro-PET process. Despite the similarities in chemical structures, the fluorescent enhancement multiple of PDI-B with aromatic amine as electron donor is much higher than that of PDI-P with alkyl amine. In the direct irradiation experiments of ionizing radiation, the emission enhancement multiples of PDI-P and PDI-B are 2.01 and 45.4, respectively. Furthermore, density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations indicate that the HOMO and HOMO-1 energy ranges of PDI-P and PDI-B are 0.54 eV and 1.13 eV, respectively. A wider energy range has a stronger driving force on electrons, which is conducive to fluorescence quenching. Both femtosecond transient absorption spectroscopy (fs-TAS) and transient fluorescence spectroscopy (TFS) tests show that PDI-B has shorter charge separation lifetime and higher electron transfer rate constant. Although both isomers can significantly reduce LOD during PET process, PDI-B with aromatic amine has a wider detection range of 0.118–240 Gy due to its larger emission enhancement, which is a leap of three orders of magnitude. It breaks through the detection range of gamma radiation reported in existing studies, and provides theoretical support for the further study of sensitive and effective new materials for ionizing radiation detection.

HCV Infection and Liver Cirrhosis Are Associated with a Less-Favorable Serum Cholesteryl Ester Profile Which Improves through the Successful Treatment of HCV.

Background: Infection with hepatitis C virus (HCV) lowers serum cholesterol levels, which rapidly recover during therapy with direct-acting antivirals (DAAs). Serum cholesterol is also reduced in patients with liver cirrhosis. Studies investigating serum cholesterol in patients with chronic liver diseases are generally based on enzymatic assays providing total cholesterol levels. Hence, these studies do not account for the individual cholesteryl ester (CE) species, which have different properties according to acyl chain length and desaturation. Methods: Free cholesterol (FC) and 15 CE species were quantified by flow injection analysis high-resolution Fourier Transform mass spectrometry (FIA-FTMS) in the serum of 178 patients with chronic HCV before therapy and during treatment with DAAs. Results: Serum CEs were low in HCV patients with liver cirrhosis and, compared to patients without cirrhosis, proportions of CE 16:0 and 16:1 were higher whereas % CE 20:4 and 20:5 were reduced. FC levels were unchanged, and the CE/FC ratio was consequently low in cirrhosis. FC and CEs did not correlate with viral load. Four CE species were reduced in genotype 3 compared to genotype 1-infected patients. During DAA therapy, 9 of the 15 measured CE species, and the CE/FC ratio, increased. Relative to total CE levels, % CE 16:0 declined and % CE 18:3 was higher at therapy end. At this time, % CE 14:0, 16:0 and 16:1 were higher and % CE 20:4 and 22:6 were lower in the cirrhosis than the non-cirrhosis patients. Viral genotype associated changes of CEs disappeared at therapy end. Conclusions: The serum CE composition differs between patients with and without liver cirrhosis, and changes through the efficient elimination of HCV. Overall, HCV infection and cirrhosis are associated with a higher proportion of CE species with a lower number of carbon atoms and double bonds, reflecting a less-favorable CE profile.

Insight into asphaltene transformation during coal tar hydrotreatment by conventional analysis and high-resolution Fourier transform mass spectrometry coupled with collision-induced dissociation technology

Asphaltenes are the heaviest and least understood fraction for the petroleum and coal-derived oil resulting in the great challenge during the hydrotreating (HDT) process. In this study, the evolution law of polar functional groups, heteroatom species and structure attributes of coal tar asphaltene was systematically studied at different temperatures using the multifunctional hydrogenation and cracking catalysts through FT-IR, XPS, 1H NMR, 13C NMR and ESI FT-ICR MS coupled with collision-induced dissociation (CID) technology. Most of S has been removed, whereas some refractory O and N are reserved in HDT asphaltenes. The temperature has a significant effect on the low reactivity heteroatom compounds, and high temperature significantly contributes to the hydrodeoxygenation reactions. The OH–OH and OH-ether O are the main hydrogen bonds in both the primary and HDT asphaltenes. The OH-π and cyclic-OH hydrogen bonds decrease with the temperature increasing, whereas that of OH–OH hydrogen bond decreases. The aromatic ether groups increase while those of CO of COOH, C–O of phenols and C–O–C groups decrease after HDT. Both the primary and HDT asphaltenes are dominant by island-type structures and the proportion of island-type fragments increases after HDT. The molecules with multiple O or N atoms are more likely to be an island-type structure in HDT asphaltenes. Besides, the heterolysis mode is the major bond cleavages path for B-NnC and B-NnOxC molecules. The heterolysis mode is the main bond cleavages path for the N-NnC, N-NnOxC and OxC molecules with less heteroatoms in HDT asphaltenes, whereas the homolytic mode dominate for poly-heteroatom molecules. Moreover, there are some “atypical” asphaltene molecules with small size and low aromaticity in both the primary and HDT asphaltenes. The “atypical” asphaltenes are dominant in the removed O1 to O5+ classes.

Glycerophospholipidomics of Five Edible Oleaginous Microgreens.

Microgreens are a special type of vegetal product, born as a culinary novelty (traditionally used to garnish gourmet dishes) and then progressively studied for their potentially high content in nutraceuticals, like polyphenolic compounds, carotenoids, and glucosinolates, also in the perspective of implementing their cultivation in space stations/colonies. Among further potential nutraceuticals of microgreens, lipids have received very limited attention so far. Here, glycerophospholipids contained in microgreens of typical oleaginous plants, namely, soybean, chia, flax, sunflower, and rapeseed, were studied using hydrophilic interaction liquid chromatography (HILIC), coupled to high-resolution Fourier transform mass spectrometry (FTMS) or low-resolution collisionally induced dissociation tandem mass spectrometry (CID-MS2) with electrospray ionization (ESI). Specifically, this approach was employed to obtain qualitative and quantitative profiling of the four main classes of glycerophospholipids (GPL) found in the five microgreens, i.e., phosphatidylcholines (PC), phosphatidylethanolamines (PE), phosphatidylglycerols (PG), and phosphatidylinositols (PI). Saturated chains with 16 and 18 carbon atoms and unsaturated 18:X (with X = 1-3) chains emerged as the most common fatty acyl substituents of those GPL; a characteristic 16:1 chain (including a C═C bond between carbon atoms 3 and 4) was also found in some PG species. Among polyunsaturated acyl chains, the 18:3 one, likely referred mainly to α-linolenic acid, exhibited a relevant incidence, with the highest estimated amount (corresponding to 160 mg per 100 g of lyophilized vegetal tissue) found for chia. This outcome opens interesting perspectives for the use of oleaginous microgreens as additional sources of essential fatty acids, especially in vegetarian/vegan diets.

Insight into the Storage-Related Oxidative/Hydrolytic Degradation of Olive Oil Secoiridoids by Liquid Chromatography and High-Resolution Fourier Transform Mass Spectrometry.

The study of negative effects potentially exerted by the exposure to oxygen and/or light and, thus, also by the type of container on the quality of extra virgin olive oil (EVOO) during its prolonged storage requires an appropriate choice of analytical methods and components to be monitored. Here, reverse-phase liquid chromatography coupled to high-resolution/accuracy Fourier transform mass spectrometry with electrospray ionization was exploited to study oxidative/hydrolytic degradation processes occurring on the important bioactive components of EVOO known as secoiridoids, i.e., oleuropein and ligstroside aglycones, oleacin, and oleocanthal, during storage up to 6 months under controlled conditions. Specifically, isomeric oxidative byproducts resulting from the transformation of a carbonylic group of the original secoiridoids into a carboxylic group and compounds resulting from hydrolysis of the ester linkage of secoiridoids, i.e., elenolic and decarboxymethyl elenolic acids and tyrosol and 3-hydroxytyrosol, were monitored, along with their precursors. Data obtained from EVOO storage at room temperature in glass bottles with/without exposure to light and/or oxygen indicated that, although it was more relevant if a periodical exposure to oxygen was performed, a non-negligible oxidative degradation occurred on secoiridoids also when nitrogen was used to saturate the container headspace. In a parallel experiment, the effects of storage of the same EVOO (250 mL) for up to 6 months in containers manufactured with different materials/shapes were considered. In particular, a square dark glass bottle, a stainless-steel can, and a ceramic jar, typically used for EVOO commercialization, and a clear polyethylene terephthalate bottle, purposely chosen to prompt secoiridoid degradation through exposure to light and oxygen, were compared. Dark glass was found to provide the best combined protection of major secoiridoids from oxidative and hydrolytic degradation, yet the lowest levels of oxidized byproducts were observed when the stainless-steel can was used.

Insights from Nitrogen Compounds in Gas Oils Highlighted by High-Resolution Fourier Transform Mass Spectrometry

Twenty-three gas oil samples from different origins were analyzed in positive and negative ion modes by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI(±)-FT-ICR MS). Sample ionization and ion transfer conditions were first optimized using Design of Experiment approach. Advanced characterization of basic and neutral nitrogen compounds in these samples was then performed through ESI(±)-FT-ICR MS analysis. A good repeatability was observed from the analysis of six replicates for each gas oil sample. Significant differences in molecular composition were spotted between the gas oils, either considering identified heteroatomic classes or within nitrogen families and were later correlated to samples macroscopic properties. The evolution of nitrogen relative intensities for one feed and two corresponding effluents has also been studied to monitor hydrotreatment reaction pathways toward aromaticity and alkylation levels evolutions.

Global Proteome Profiling Reveals Drug-Resistant Traits in Elizabethkingia meningoseptica: An Opportunistic Nosocomial Pathogen.

Elizabethkingia meningoseptica is Gram-negative, rod-shaped opportunistic bacterial pathogen increasingly reported in hospital-acquired outbreaks. This bacterium is well known to thrive in the hospital environment. One of the leading causes of meningitis in pediatric and immune-compromised patients, E. meningoseptica has been noted as a "pathogen of interest" in the context of nosocomial diseases associated with device-related infections in particular. This pathogen's multidrug-resistant phenotype and attendant lack of adequate molecular mechanistic data limit the current approaches for its effective management in hospitals and public health settings. This study provides the global proteome of E. meningoseptica. The reference strain E. meningoseptica ATCC 13253 was used for proteomic analysis using high-resolution Fourier transform mass spectrometry. The study provided translational evidence for 2506 proteins of E. meningoseptica. We identified multiple metallo-β-lactamases, transcriptional regulators, and efflux transporter proteins associated with multidrug resistance. A protein Car D, which is an enzyme of the carbapenem synthesis pathway, was also discovered in E. meningoseptica. Further, the proteomics data were harnessed for refining the genome annotation. We discovered 39 novel protein-coding genes and corrected four existing translations using proteogenomic workflow. Novel translations reported in this study enhance the molecular data on this organism, thus improving current databases. We believe that the in-depth proteomic data presented in this study offer a platform for accelerated research on this pathogen. The identification of multiple proteins, particularly those involved in drug resistance, offers new future opportunities to design novel and specific antibiotics against infections caused by E. meningoseptica.

Speciation of structural fragments in crude oil by means of isotope exchange in near-critical water and Fourier transform mass spectrometry.

The structures of individual molecules in crude oil remain largely unknown despite the considerable amount of research dedicated to this topic. The extreme complexity of crude oil (recently Marshall reported the observation of more than 400,000 unique compounds in one sample) makes it impossible to separate crude oil into individual compounds and determine their structure by NMR or X-ray spectroscopy. Recently, isotope exchange, performed both in solution and in the gas phase, combined with high-resolution mass spectrometry was used for speciation of certain structural fragments of individual molecules in crude oil and humic substances. 16O/18O exchange allows enumeration of =O groups and speciation of furans, whereas H/D exchange allows enumeration of -OH groups, -NH groups, aromatic hydrogens, alpha hydrogens, etc. Unfortunately, crude oil is insoluble in water (the most available and cleanest source of isotopes), so performance of the exchange in solution requires harsh conditions, such as concentrated acids or bases, which could considerably modify the sample. Here we describe the use of a cheap and simple analytical approach for performing both H/D and 16O/18O exchange in crude oil using only water as the source of the isotopes. Crude oil was incubated in near-critical water and the reaction was monitored by high-resolution Fourier transform mass spectrometry. Although isotope exchange results in complication of the spectrum, the resolving power of modern mass spectrometers is sufficient to determine the number of exchanges for each molecule simultaneously. We determined the number of 16O/18O exchanges in 276 species and the number of H/D exchanges in 150 species. Our results allow deeper investigation of crude oil and other nonpolar samples on the molecular level. Graphical abstract.

Quantification of Cholesterol and Cholesteryl Ester by Direct Flow Injection High-Resolution Fourier Transform Mass Spectrometry Utilizing Species-Specific Response Factors.

The quantification of free cholesterol (FC) and cholesteryl ester (CE) in mammalian samples is of great interest for basic science and clinical lipidomics. Here, we evaluated the feasibility of direct flow injection analysis (FIA) coupled to electrospray ionization high-resolution mass spectrometry (ESI-HRMS) to quantify FC and CE in lipid extracts from human serum, cultured cells, and mouse liver. Despite poor ionization efficiency of FC, the limit of quantitation was sufficient for precise and accurate quantification of FC by multiplexed HRMS (MSX) analysis without using a derivatization step. However, it was demonstrated that, upon full scan Fourier transform MS (FTMS) quantification, CE species show substantial differences in their analytical responses depending on number of double bonds, length of the acyl chain, infused lipid concentration, and other lipid components. A major determinant for these response differences is their susceptibility to in-source fragmentation. In particular, introduction of double bonds lowers the degree of in-source fragmentation. Therefore, CE species-specific response factors need to be applied for CE quantification by FTMS to achieve accurate concentrations. Method validation demonstrated that FIA-ESI-HRMS (MSX and FTMS) is applicable for quantification of FC and CE in samples used in basic science as well as clinical studies such as cultured cells, tissue homogenates, and serum.

Proteomic Analysis of the Human Anterior Pituitary Gland.

The pituitary function is regulated by a complex system involving the hypothalamus and biological networks within the pituitary. Although the hormones secreted from the pituitary have been well studied, comprehensive analyses of the pituitary proteome are limited. Pituitary proteomics is a field of postgenomic research that is crucial to understand human health and pituitary diseases. In this context, we report here a systematic proteomic profiling of human anterior pituitary gland (adenohypophysis) using high-resolution Fourier transform mass spectrometry. A total of 2164 proteins were identified in this study, of which 105 proteins were identified for the first time compared with high-throughput proteomic-based studies from human pituitary glands. In addition, we identified 480 proteins with secretory potential and 187 N-terminally acetylated proteins. These are the first region-specific data that could serve as a vital resource for further investigations on the physiological role of the human anterior pituitary glands and the proteins secreted by them. We anticipate that the identification of previously unknown proteins in the present study will accelerate biomedical research to decipher their role in functioning of the human anterior pituitary gland and associated human diseases.

Metabolomics-Coupled Functional Pharmacology of Chlorophyll Compounds Isolated From the Leaves of Ficus Exasperata Vahl (Moraceae) Provides Novel Pathways on Myometrial Activity

New chlorophyll derivatives (pheophytins along with pheophorbide derivatives) were isolated from the leaves of Ficus exasperata and were found to have varying effects on uterine contractility. The current study was therefore aimed at the utilization of mass spectrometry and nuclear magnetic resonance spectroscopy coupled with isolated uterine tissue assay as a platform to assist in the determination of the mechanism of activity of the isolated chlorophyll compounds from the plant F exasperata. The pheophytin and pheophorbide compounds (200 µg/mL) were added to the isolated uterine tissues. Mice uteri, treated with the pheophytin compounds, and the physiological buffer in which the uterine tissues were immersed, were rapidly collected and analyzed using high-resolution Fourier transform mass spectrometry and proton (1H) nuclear magnetic resonance for bioinformatics study. Resulting data were analyzed via pairwise chemometric comparison models, with P < .05 considered statistically significant. Primary signaling pathways found to be correlated with the pheophytins in this study included cyclic adenosine monophosphate, dopamine, extracellular signal-regulated kinases 1/2, and glutamate pathways.

Exosomal lipids for classifying early and late stage non-small cell lung cancer

Lung cancer is the leading cause of cancer deaths in the United States. Patients with early stage lung cancer have the best prognosis with surgical removal of the tumor, but the disease is often asymptomatic until advanced disease develops, and there are no effective blood-based screening methods for early detection of lung cancer in at-risk populations. We have explored the lipid profiles of blood plasma exosomes using ultra high-resolution Fourier transform mass spectrometry (UHR-FTMS) for early detection of the prevalent non-small cell lung cancers (NSCLC). Exosomes are nanovehicles released by various cells and tumor tissues to elicit important biofunctions such as immune modulation and tumor development. Plasma exosomal lipid profiles were acquired from 39 normal and 91 NSCLC subjects (44 early stage and 47 late stage). We have applied two multivariate statistical methods, Random Forest (RF) and Least Absolute Shrinkage and Selection Operator (LASSO) to classify the data. For the RF method, the Gini importance of the assigned lipids was calculated to select 16 lipids with top importance. Using the LASSO method, 7 features were selected based on a grouped LASSO penalty. The Area Under the Receiver Operating Characteristic curve for early and late stage cancer versus normal subjects using the selected lipid features was 0.85 and 0.88 for RF and 0.79 and 0.77 for LASSO, respectively. These results show the value of RF and LASSO for metabolomics data-based biomarker development, which provide robust an independent classifiers with sparse data sets. Application of LASSO and Random Forests identifies lipid features that successfully distinguish early stage lung cancer patient from healthy individuals.

Toward Understanding Myometrial Regulation: Metabolomic Investigation Reveals New Pathways of Oxytocin and Ritodrine Activity on the Myometrium.

In recent times, additional pathways involved in the regulation of the myometrium have been suggested. This also holds true for the effect of drugs such as oxytocin (OT) and β-adrenergic agonists on the myometrium. Knowledge of these additional pathways will certainly prove useful in designing better therapies for pathologies of the myometrium. This study was therefore aimed at investigating the possibility of other pathways involved in the activities of both OT and ritodrine (RIT; a β-adrenergic agonist) in the myometrium by utilizing metabolomics and bioinformatics. High-resolution Fourier transform mass spectrometry (HRFTMS) and nuclear magnetic resonance (NMR) spectroscopy coupled with functional uterine assays were used for an innovative assessment. In vitro pharmacological assay of OT (1 nmol/L) and RIT (0.1 nmol/L) on isolated mice uteri mounted in 3 mL organ baths was performed. Mice uteri, treated with OT or RIT, as well as the physiological buffer in which the uterine tissues were immersed, were rapidly collected and analyzed using HRFTMS, proton (1H)-NMR, and bioinformatics. Resulting data were analyzed via pairwise chemometric comparison models, with P ≤ .05 considered statistically significant. In addition to previously known metabolites, nicotinamide adenine dinucleotide, γ-aminobutyric acid, and sphingosine were significantly associated with the activity of OT, whereas the activity of RIT was associated with a downstream involvement of prostaglandin F1 and phosphatidylinositol signaling. These findings add evidence to the reports on additional regulation of myometrial activity by these drugs and suggest newer pathways for therapeutic manipulation.

Quantitative Proteomic and Phosphoproteomic Analysis of H37Ra and H37Rv Strains of Mycobacterium tuberculosis.

Mycobacterium tuberculosis, the causative agent of tuberculosis, accounts for 1.5 million human deaths annually worldwide. Despite efforts to eradicate tuberculosis, it still remains a deadly disease. The two best characterized strains of M. tuberculosis, virulent H37Rv and avirulent H37Ra, provide a unique platform to investigate biochemical and signaling pathways associated with pathogenicity. To delineate the biomolecular dynamics that may account for pathogenicity and attenuation of virulence in M. tuberculosis, we compared the proteome and phosphoproteome profiles of H37Rv and H37Ra strains. Quantitative phosphoproteomic analysis was performed using high-resolution Fourier transform mass spectrometry. Analysis of exponential and stationary phases of these strains resulted in identification and quantitation of 2709 proteins along with 512 phosphorylation sites derived from 257 proteins. In addition to confirming the presence of previously described M. tuberculosis phosphorylated proteins, we identified 265 novel phosphorylation sites. Quantitative proteomic analysis revealed more than five-fold upregulation of proteins belonging to virulence associated type VII bacterial secretion system in H37Rv when compared to those in H37Ra. We also identified 84 proteins, which exhibited changes in phosphorylation levels between the virulent and avirulent strains. Bioinformatics analysis of the proteins altered in their level of expression or phosphorylation revealed enrichment of pathways involved in fatty acid biosynthesis and two-component regulatory system. Our data provides a resource for further exploration of functional differences at molecular level between H37Rv and H37Ra, which will ultimately explain the molecular underpinnings that determine virulence in tuberculosis.

Marine Sponge-Derived Streptomyces sp. SBT343 Extract Inhibits Staphylococcal Biofilm Formation.

Staphylococcus epidermidis and Staphylococcus aureus are opportunistic pathogens that cause nosocomial and chronic biofilm-associated infections. Indwelling medical devices and contact lenses are ideal ecological niches for formation of staphylococcal biofilms. Bacteria within biofilms are known to display reduced susceptibilities to antimicrobials and are protected from the host immune system. High rates of acquired antibiotic resistances in staphylococci and other biofilm-forming bacteria further hamper treatment options and highlight the need for new anti-biofilm strategies. Here, we aimed to evaluate the potential of marine sponge-derived actinomycetes in inhibiting biofilm formation of several strains of S. epidermidis, S. aureus, and Pseudomonas aeruginosa. Results from in vitro biofilm-formation assays, as well as scanning electron and confocal microscopy, revealed that an organic extract derived from the marine sponge-associated bacterium Streptomyces sp. SBT343 significantly inhibited staphylococcal biofilm formation on polystyrene, glass and contact lens surfaces, without affecting bacterial growth. The extract also displayed similar antagonistic effects towards the biofilm formation of other S. epidermidis and S. aureus strains tested but had no inhibitory effects towards Pseudomonas biofilms. Interestingly the extract, at lower effective concentrations, did not exhibit cytotoxic effects on mouse fibroblast, macrophage and human corneal epithelial cell lines. Chemical analysis by High Resolution Fourier Transform Mass Spectrometry (HRMS) of the Streptomyces sp. SBT343 extract proportion revealed its chemical richness and complexity. Preliminary physico-chemical characterization of the extract highlighted the heat-stable and non-proteinaceous nature of the active component(s). The combined data suggest that the Streptomyces sp. SBT343 extract selectively inhibits staphylococcal biofilm formation without interfering with bacterial cell viability. Due to absence of cell toxicity, the extract might represent a good starting material to develop a future remedy to block staphylococcal biofilm formation on contact lenses and thereby to prevent intractable contact lens-mediated ocular infections.

Comprehensive Proteomic Characterization of the Human Colorectal Carcinoma Reveals Signature Proteins and Perturbed Pathways

The global change in protein abundance in colorectal cancer (CRC) and its contribution to tumorigenesis have not been comprehensively analyzed. In this study, we conducted a comprehensive proteomic analysis of paired tumors and adjacent tissues (AT) using high-resolution Fourier-transform mass spectrometry and a novel algorithm of quantitative pathway analysis. 12380 proteins were identified and 740 proteins that presented a 4-fold change were considered a CRC proteomic signature. A significant pattern of changes in protein abundance was uncovered which consisted of an imbalance in protein abundance of inhibitory and activating regulators in key signal pathways, a significant elevation of proteins in chromatin modification, gene expression and DNA replication and damage repair, and a decreased expression of proteins responsible for core extracellular matrix architectures. Specifically, based on the relative abundance, we identified a panel of 11 proteins to distinguish CRC from AT. The protein that showed the greatest degree of overexpression in CRC compared to AT was Dipeptidase 1 (DPEP1). Knockdown of DPEP1 in SW480 and HCT116 cells significantly increased cell apoptosis and attenuated cell proliferation and invasion. Together, our results show one of largest dataset in CRC proteomic research and provide a molecular link from genomic abnormalities to the tumor phenotype.

Hydrophilic interaction and reversed phase mixed-mode liquid chromatography coupled to high resolution tandem mass spectrometry for polar lipids analysis

A hydrophilic interaction liquid chromatography (HILIC) fused-core column (150×2.1mm ID, 2.7μm particle size) and a short reversed-phase liquid chromatography (RPLC) column (20mm×2.1mm ID, 1.9μm) were serially coupled to perform mixed-mode chromatography (MMC) on complex mixtures of phospholipids (PL). Mobile phase composition and gradient elution program were, preliminarily, optimized using a mixture of phosphatidylcholines (PC), phosphatidylethanolamines (PE), their corresponding lyso-forms (LPC and LPE), and sphingomyelins (SM). Thus a mixture of PC extracted from soybean was characterized by MMC coupled to electrospray ionization (ESI) high-resolution Fourier-transform mass spectrometry (FTMS) using an orbital trap analyzer. Several previously undiscovered PC, including positional isomers (i.e. 16:0/19:1 and 19:1/16:0) of PC 35:1 and skeletal isomers (i.e. 18:1/18:2 and 18:0/18:3) of PC 36:3 were identified. Therefore, high-resolution MS/MS spectra unveiled the occurrence of isomers for several overall side chain compositions. The proposed MMC-ESI-FTMS/MS approach revealed an unprecedented capability in disclosing complexity of an actual lipid extract, thus representing a very promising approach to lipidomics.

A Comprehensive Proteomics Analysis of the Human Iris Tissue: Ready to Embrace Postgenomics Precision Medicine in Ophthalmology?

The annual economic burden of visual disorders in the United States was estimated at $139 billion. Ophthalmology is therefore one of the salient application fields of postgenomics biotechnologies such as proteomics in the pursuit of global precision medicine. Interestingly, the protein composition of the human iris tissue still remains largely unexplored. In this context, the uveal tract constitutes the vascular middle coat of the eye and is formed by the choroid, ciliary body, and iris. The iris forms the anterior most part of the uvea. It is a thin muscular diaphragm with a central perforation called pupil. Inflammation of the uvea is termed uveitis and causes reduced vision or blindness. However, the pathogenesis of the spectrum of diseases causing uveitis is still not very well understood. We investigated the proteome of the iris tissue harvested from healthy donor eyes that were enucleated within 6 h of death using high-resolution Fourier transform mass spectrometry. A total of 4959 nonredundant proteins were identified in the human iris, which included proteins involved in signaling, cell communication, metabolism, immune response, and transport. This study is the first attempt to comprehensively profile the global proteome of the human iris tissue and, thus, offers the potential to facilitate biomedical research into pathological diseases of the uvea such as Behcet's disease, Vogt Koyonagi Harada's disease, and juvenile rheumatoid arthritis. Finally, we make a call to the broader visual health and ophthalmology community that proteomics offers a veritable prospect to obtain a systems scale, functional, and dynamic picture of the eye tissue in health and disease. This knowledge is ultimately pertinent for precision medicine diagnostics and therapeutics innovation to address the pressing needs of the 21st century visual health.

Proteogenomics of Candida tropicalis--An Opportunistic Pathogen with Importance for Global Health.

The frequency of Candida infections is currently rising, and thus adversely impacting global health. The situation is exacerbated by azole resistance developed by fungal pathogens. Candida tropicalis is an opportunistic pathogen that causes candidiasis, for example, in immune-compromised individuals, cancer patients, and those who undergo organ transplantation. It is a member of the non-albicans group of Candida that are known to be azole-resistant, and is frequently seen in individuals being treated for cancers, HIV-infection, and those who underwent bone marrow transplantation. Although the genome of C. tropicalis was sequenced in 2009, the genome annotation has not been supported by experimental validation. In the present study, we have carried out proteomics profiling of C. tropicalis using high-resolution Fourier transform mass spectrometry. We identified 2743 proteins, thus mapping nearly 44% of the computationally predicted protein-coding genes with peptide level evidence. In addition to identifying 2591 proteins in the cell lysate of this yeast, we also analyzed the proteome of the conditioned media of C. tropicalis culture and identified several unique secreted proteins among a total of 780 proteins. By subjecting the mass spectrometry data derived from cell lysate and conditioned media to proteogenomic analysis, we identified 86 novel genes, 12 novel exons, and corrected 49 computationally-predicted gene models. To our knowledge, this is the first high-throughput proteomics study of C. tropicalis validating predicted protein coding genes and refining the current genome annotation. The findings may prove useful in future global health efforts to fight against Candida infections.