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Protein phosphorylation plays critical roles in diverse cellular functions, including cell cycle, growth, differentiation, and apoptosis. Deregulated phospho-signaling is often associated with many human diseases and cancers. Despite tremendous efforts to investigate the molecular mechanisms that control the functionality of phospho-signaling pathways, only limited progress has been made on describing the temporal and spatial profiles of cellular protein phosphorylation. The main challenges associated with the study of phospho-signaling processes in cells are related to the short time-scale of certain phosphorylation and dephosphorylation events, the low abundance of the phosphorylated protein forms as compared to their non-phosphorylated counterparts, the complicated and time-consuming sample preparation methods that are accompanying such type of work, and, last, the performance of the detection methods that are suitable for assessing protein phosphorylation. To tackle the challenges associated with the investigation of protein phosphorylation in cells, our objective was to develop a combined mass spectrometry (MS) and microfluidics strategy that enables fast sampling and sensitive detection of key signaling phosphoproteins in complex biological samples. MS is the most widely used analytical tool in the field of proteomics due to its high sensitivity, specificity, and throughput. Microfluidics has been proven as a suitable platform for handling small volumes of scarce samples, being also amenable to automation, integration, and multiplexing. To achieve our objective, this study was conducted in multiple steps: (1) We performed a comprehensive analysis of the factors that affect the performance of mass spectrometry detection (i.e., sensitivity, reproducibility, ability to accurately identify a large number of proteins from complex samples), when used in conjunction with technologies that are conducted in a non-standard fashion, on short time-scales; (2) We developed and evaluated a miniaturized strategy for rapid proteolytic digestion and phosphopeptide enrichment; (3) We demonstrated sensitive detection and quantification of phosphopeptides from complex biological samples using multiple reaction monitoring mass spectrometry (MRM-MS) and microfluidic sample processing; and (4) We developed a microfluidic platform for handling and processing cells that enables the investigation of biological processes that occur on short time-scales, and that can be integrated with the devices developed for the analysis of phospho-proteins. SKBR3 cells were used as a model system for developing and demonstrating the microfluidic chips. The detection and quantification of phospho-proteins involved in MAPK (mitogen activated protein kinase) signaling pathways was achieved at the low nM level. Overall, this study demonstrates proof-of-concept applicability of a microfluidics-MS strategy for monitoring phosphorylation processes in signaling networks. / PHD / Cellular protein phosphorylation plays critical roles in cellular functions, and deregulated phosphorylation is often associated with many human diseases and cancers. Despite tremendous efforts to investigate the molecular mechanisms that control cellular protein phosphorylation events, limited progress has been made on describing the temporal and spatial profiles. The main challenges are related to the short time-scale of certain phosphorylation and dephosphorylation events, the low abundance of the phosphorylated protein forms as compared to their non-phosphorylated counterparts, the complicated and time-consuming sample preparation methods that are accompanying such type of work, and, last, the performance of the detection methods that are suitable for assessing protein phosphorylation. To address the issues involved in the investigation of protein phosphorylation in cells, we developed a novel strategy using mass spectrometry (MS) and microfluidics. This study was conducted in multiple steps: (1) We performed a comprehensive analysis of the factors that affect the performance of mass spectrometry detection; (2) We developed and evaluated a miniaturized strategy for rapid proteolytic digestion and phosphopeptide enrichment; (3) We demonstrated sensitive detection and quantification of phosphopeptides from complex biological samples; and (4) We developed a microfluidic platform for handling and processing cells that enables the investigation of biological processes that occur on short time-scales, and that can be integrated with the devices developed for the analysis of phospho-proteins.

In the United States, breast cancer is the most commonly diagnosed cancer and is the second most common cause of cancer-related deaths among women. Among the various subtypes of breast cancer, 25-30% of diagnoses present themselves as human epidermal growth factor receptor 2 positive (HER-2+). HER-2 is a protein receptor located on the cell surface that interacts with other proteins and signaling molecules to translate extracellular signals into cellular process such as cell growth and replication. However, in breast cancer, there is a drastic increase in the number of HER-2 proteins on the cell surface, that causes excessive cell growth and proliferation, and ultimately tumor formation. The most frequent treatment of HER-2+ breast cancers includes the use of a single agent inhibitor that directly blocks the HER-2 protein to prevent over-signaling and cell growth. However, after continuous use, breast cancer cells develop drug resistance, as other proteins such as the insulin-like growth factor 1 receptor (IGF-1R) and the protein kinase B (AKT) can also interfere and cause cell growth and replication. In this study, we propose that the use of a multi-agent treatment targeting the HER-2, IGF-1R, and AKT proteins will be more effective than a single-agent treatment of HER-2 alone. Through protein analysis by mass spectrometry, we intend to illuminate the different cellular responses to both treatment types. The results indicate that the single drug treatment targeting Her-2 appears to increase processes related cellular repair, while the multi-drug treatment indicates an increase in processes related to programmed cell death; both treatments appear to block the transmission of protein signaling. / MS / In the United States, breast cancer is the most commonly diagnosed cancer and is the second most common cause of cancer-related deaths among women. Among the various subtypes of breast cancer, 25-30% of diagnoses present themselves as human epidermal growth factor receptor 2 positive (HER-2+). HER-2 is a protein receptor located on the cell surface that interacts with other proteins and signaling molecules to translate extracellular signals into cellular process such as cell growth and replication. However, in breast cancer, there is a drastic increase in the number of HER-2 proteins on the cell surface, that causes excessive cell growth and proliferation, and ultimately tumor formation. The most frequent treatment of HER-2+ breast cancers includes the use of a single agent inhibitor that directly blocks the HER-2 protein to prevent over-signaling and cell growth. However, after continuous use, breast cancer cells develop drug resistance, as other proteins such as the insulin-like growth factor 1 receptor (IGF-1R) and the protein kinase B (AKT) can also interfere and cause cell growth and replication. In this study, we propose that the use of a multi-agent treatment targeting the HER-2, IGF-1R, and AKT proteins will be more effective than a single-agent treatment of HER-2 alone. Through protein analysis by mass spectrometry, we intend to illuminate the different cellular responses to both treatment types. The results indicate that the single drug treatment targeting Her-2 appears to increase processes related cellular repair, while the multi-drug treatment indicates an increase in processes related to programmed cell death; both treatments appear to block the transmission of protein signaling.

No / SJG-136 is a synthetic pyrrolobenzodiazepine (PBD) dimer in which two DNA-alkylating subunits are linked through an inert propanedioxy tether. Biophysical and biochemical studies of SJG-136 have shown a remarkable affinity for DNA and potent cytotoxicity in vitro. On this basis, together with its unique sequence selectivity and interstrand DNA cross-linking activity, SJG-136 has been selected for clinical trials. This study examines the pharmacological characteristics of SJG-136 and provides the first report of pharmacokinetic properties for this agent. A sensitive, selective and reproducible reversed-phase gradient LC/MS assay has been developed for detection and analysis, where a molecular ion ( m / z 557.2) is detectable for the SJG-136 parent imine. Fluorescence detection (260 nm excitation, 420 nm emission) gives a limit of sensitivity of 5 nM (2.5 ng ml(-1)) for analysis of SJG-136 in mouse plasma. Extraction efficiencies from plasma were >65% across a range of concentrations (5-1000 nM). Following administration to mice at the MTD (i.p., 0.2 mg kg(-1)), high peak plasma concentrations of SJG-136 were seen ( C (max) = 336 nM) at 30 min after dosing. A calculated terminal t (1/2) of 0.98 h and AUC of 0.34 microM.h resulted in a clearance rate of 17.7 ml min(-1) kg(-1). The PBD dimer binds only moderately to proteins (65-75%), and in vitro cytotoxicity studies confirmed IC(50) values of 4-30 nM with a panel of human cell lines. This finding demonstrates that plasma concentrations achieved in the mouse are substantially higher than those required to elicit an anti tumour response in vitro. This report forms an important phase in the pre-clinical characterization of the compound.

No / The structural and functional diversity of lipids accounts for their involvement into a wide range of homeostatic processes and disease states, including lifestyle-related diseases as well as genetic conditions. Challenges presented by this diversity have been addressed to a great extent by the development of lipidomics, a platform that makes possible the detailed profiling and characterisation of lipid species present in any cell, organelle, tissue or body fluid, and allows for a wider appreciation of the biological role of lipid networks. Progress in the field of lipidomics has been greatly facilitated by recent advances in MS and includes a range of analytical platforms supporting applications spanning from qualitative and quantitative assessment of multiple species to lipid imaging. Here we review these MS techniques currently in routine use in lipidomics, alongside with new ones that have started making an impact in the field. Recent applications in health, disease and nutrition-related questions will also be discussed with a view to convey the importance of lipidomics contributions to biosciences and food technology.

No / Hypoxia is a common feature observed in solid tumours. It is a target of interest in oncology as it has been found to be closely associated with tumour progression, metastasis and aggressiveness and confers resistance to a variety of chemotherapeutic agents as well as radiotherapy. AQ4N, also known as banoxatrone or 1,4-bis-[2-(dimethylamino-Noxide) ethyl]amino-5,8-dihydroxyanthracene-9,10-dione is a very promising bioreductive prodrug. This paper, describes an application of MALDI-MSI combined with ion mobility separation and an "on-tissue" bottom up proteomic strategy to obtain proteomic data from AQ4N dosed tumour xenograft tissue sections. These data are then correlated with the drug distribution determined also using MALDI-ion mobility separation-mass spectrometry imaging (MALDI-IMS-MSI). PCA-DA and OPLS-DA have been used to compare treated and untreated xenografts and of note is the marked increase in expression of Histone H3.

Yes / As pre-clinical and clinical research interest in ω-3 polyunsaturated fatty acids (PUFA) increases, so does the need for a fast, accurate and reproducible analytical method to measure fatty acids (FA) in biological samples in order to validate potential prognostic and predictive biomarkers, as well as establishing compliance in ω-3 PUFA intervention trials. We developed a LC-ESI-MS/MS method suitable for high throughput development to measure FAs and validated it in the context of treatment with the ω-3 PUFA eicosapentaenoic acid (EPA). Uniquely we directly compared the LC-ESI-MS/MS method to a GC-MS protocol. We demonstrated the LC-ESI-MS/MS method is accurate and reproducible, with coefficients of variation consistently below 15% for each PUFA analysed. The relative FA content values correlated well with those obtained by GC-MS (r2 = 0.94, p<0.001 for EPA) in vitro. The data obtained following analysis of FA content of liver tissues from mice fed an eicosapentaenoic acid enriched diet showed similar results to that of published studies in which GC-MS was used. The LC-ESI-MS/MS method allows concomitant analysis of unesterified (free, unbound) and esterified (bound) FAs in biological samples, allowing investigation of different PUFA pools in cells and tissues. / Yorkshire Cancer Research, MRC/NIHR

Yes / Adequate drug distribution through tumours is essential for treatment to be effective. Palbociclib is a cyclin-dependent kinase (CDK) 4/6 inhibitor approved for use in patients with hormone receptor (HR) positive, HER2 negative metastatic breast cancer (BC). It has unusual physicochemical properties, which may significantly influence its distribution in tumour tissue. We studied the penetration and distribution of palbociclib in vitro, including the use of multicellular three-dimensional models and mathematical modelling. MCF-7 and DLD-1 cell lines were grown as single cell suspensions (SCS) and spheroids; palbociclib uptake and efflux were studied using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Intracellular concentrations of palbociclib for MCF-7 SCS (Cmax 3.22 µM) and spheroids (Cmax 2.91 µM) were 32 and 29 fold higher and in DLD-1, 13 and 7 fold higher, respectively than the media concentration (0.1 µM). Total palbociclib uptake was lower in DLD-1 cells than MCF-7 cells both in SCS and in spheroids. Both uptake and efflux of palbociclib were slower in spheroids than SCS. These data were used to develop a mathematical model of palbociclib transport that quantifies key parameters determining drug penetration and distribution. The model reproduced qualitatively most features of the experimental data and distinguished between SCS and spheroids, providing additional support for hypotheses derived from the experimental data. Mathematical modelling has the potential for translating in vitro data into clinically relevant estimates of tumour drug concentrations. / Grant for Translational Research and a grant from Leeds NHS Charitable Trustees.

No / Proteomic analysis of breast cancer tissue has proven difficult due to its inherent histological complexity. This pilot study presents preliminary evidence for the ability to differentiate adenoma and invasive carcinoma by measuring changes in proteomic profile of matched normal and disease tissues. A dual lysis buffer method was used to maximize protein extraction from each biopsy, proteins digested with trypsin, and the resulting peptides iTRAQ labeled. After combining, the peptide mixtures they were separated using preparative IEF followed by RP nanoHPLC. Following MALDI MS/MS and database searching, identified proteins were combined into a nonredundant list of 481 proteins with associated normal/tumor iTRAQ ratios for each patient. Proteins were categorized by location as blood, extracellular, and cellular, and the iTRAQ ratios were normalized to enable comparison between patients. Of those proteins significantly changed (upper or lower quartile) between matched normal and disease tissues, those from two invasive carcinoma patients had >50% in common with each other but <22% in common with an adenoma patient. In invasive carcinoma patients, several cellular and extracellular proteins that were significantly increased (Periostin, Small breast epithelial mucin) or decreased (Kinectin) have previously been associated with breast cancer, thereby supporting this approach for a larger disease-stage characterization effort.

Poor medical adherence attributed to patient compliance has impacted the medical community, at times, in a deleterious fashion. To combat this, the medical community has attempted to provide therapeutics in the form of absorption enhancing techniques. To improve the absorption rate techniques such as drug encapsulation using proteins, liposomes, or nanotransfersomes have been developed using mass spectrometry. These techniques, have aided in the enhanced absorption of analytes with low bioavailability, including curcumin, simvastatin, and lysozyme. Specifically, mass spectrometry allows for the development and monitoring of nanotransfersome encapsulated analytes and the permeation across the dermal membrane. This transdermal delivery would eliminate the problems encountered during first pass metabolism, while allowing for higher concentrations of analyte to be maintained in the blood serum. This can be coupled to a thermosensitive gelatin that provides for a dose control mechanism to be accomplished, allowing multiple doses to be delivered using one transdermal patch system. The novel delivery system developed using mass spectrometry, allows the analyte to be delivered into the circulatory system at a controlled dosage, via transdermal absorption. This system will aid in eliminating problems associated with patient compliance, as the patient is no longer reliant on memory to self-dose. Further, this system mitigates the concerns of patients overdosing with more potent pharmaceuticals.