Clinical translation of MS-based,quantitative plasma proteomics: status,challenges, requirements,and potential

Introduction: Aided by the advent of advanced mass spectrometry (MS)-based technologies and methodologies, quantitative proteomics has emerged as a viable technique to capture meaningful data for candidate biomarker evaluation. To aid clinical translation, these methods generally utilize a bottom-up strategy with isotopically labeled standards and a targeted form of MS measurement.

Areas covered: This article reviews the status, challenges, requirements, and potential of translating current, MS-based methods to the clinical laboratory. The described methods are discussed and contrasted within a fit-for-purpose approach, while different resources for quality control, quantitative analysis, and data interpretation are additionally provided.

Expert commentary: Although great strides have been made over the past five years in developing reliable quantitative assays for plasma protein biomarkers, it is crucial for investigators to have an understanding of the clinical validation process, a major roadblock in translational research. Continued progress in method design and validation of protein assays is necessary to ultimately achieve widespread adoption and regulatory approval.     

UPLC-3Q MSMRM模式在Jurkat细胞脂质代谢物监测中应用

目的：以药物干预前后的Jurkat细胞为样本,旨在找出能够有效干预淋巴瘤的药物及与淋巴瘤相关的代谢及信号通路。方法：以UPLC-3Q MS为技术平台,通过多反应监测（Multiple Reaction Monitoring,MRM）扫描模式,根据实验室前期淋巴瘤代谢组学的研究成果,选择对淋巴瘤患者和健康对照组分类有显著贡献的脂类差异代谢物作为监测对象,对PI3K inhibitor干预前后的Jurkat细胞内这些潜在的生物标记物进行定量研究。结果：PI3K inhibitor与Jurkat细胞作用一段时间后,所监测的四个脂质代谢物含量呈现出与药物干预前肿瘤组相反的变化趋势,药物干预后细胞内含量有明显先升高再降低的趋势。结论：说明PI3K介导的信号通路在淋巴瘤细胞内被放大,选择性抑制该通路可以有效抑制肿瘤增殖和肿瘤细胞的代谢活动,为淋巴瘤的临床研究提供依据。     

Coenzyme Q supplementation or over-expression of the yeast Coq8 putative kinase stabilizes multi-subunit Coq polypeptide complexes in yeast coq null mutants

Coenzyme Q biosynthesis in yeast requires a multi-subunit Coq polypeptide complex. Deletion of any one of the COQ genes leads to respiratory deficiency and decreased levels of the Coq4, Coq6, Coq7, and Coq9 polypeptides, suggesting that their association in a high molecular mass complex is required for stability. Over-expression of the putative Coq8 kinase in certain coq null mutants restores steady-state levels of the sensitive Coq polypeptides and promotes the synthesis of late-stage Q-intermediates. Here we show that over-expression of Coq8 in yeast coq null mutants profoundly affects the association of several of the Coq polypeptides in high molecular mass complexes, as assayed by separation of digitonin extracts of mitochondria by two-dimensional blue-native/SDS PAGE. The Coq4 polypeptide persists at high molecular mass with over-expression of Coq8 in coq3, coq5, coq6, coq7, coq9, and coq10 mutants, indicating that Coq4 is a central organizer of the Coq complex. Supplementation with exogenous Q₆ increased the steady-state levels of Coq4, Coq7, and Coq9, and several other mitochondrial polypeptides in select coq null mutants, and also promoted the formation of late-stage Q-intermediates. Q supplementation may stabilize this complex by interacting with one or more of the Coq polypeptides. The stabilizing effects of exogenously added Q₆ or over-expression of Coq8 depend on Coq1 and Coq2 production of a polyisoprenyl intermediate. Based on the observed interdependence of the Coq polypeptides, the effect of exogenous Q₆, and the requirement for an endogenously produced polyisoprenyl intermediate, we propose a new model for the Q-biosynthetic complex, termed the CoQ-synthome.     

4-Methylumbelliferone inhibits hyaluronan synthesis by depletion of cellular UDP-glucuronic acid and downregulation of hyaluronan synthase 2 and 3

Hyaluronan accumulation on cancer cells and their surrounding stroma predicts an unfavourable disease outcome, suggesting that hyaluronan enhances tumor growth and spreading. 4-Methylumbelliferone (4-MU) inhibits hyaluronan synthesis and retards cancer spreading in experimental animals through mechanisms not fully understood. These mechanisms were studied in A2058 melanoma cells, MCF-7 and MDA-MB-361 breast, SKOV-3 ovarian and UT-SCC118 squamous carcinoma cells by analysing hyaluronan synthesis, UDP-glucuronic acid (UDP-GlcUA) content, and hyaluronan synthase (HAS) mRNA levels. The maximal inhibition in hyaluronan synthesis ranged 22-80% in the cell lines tested. Active glucuronidation of 4-MU produced large quantities of 4-MU-glucuronide, depleting the cellular UDP-GlcUA pool. The maximal reduction varied between 38 and 95%. 4-MU also downregulated HAS mRNA levels: HAS3 was 84-60% lower in MDA-MB-361, A2058 and SKOV-3 cells. HAS2 was the major isoenzyme in MCF-7 cells and lowered by 81%, similar to 88% in A2058 cells. These data indicate that both HAS substrate and HAS2 and/or HAS3 mRNA are targeted by 4-MU. Despite different target point sensitivities, the reduction of hyaluronan caused by 4-MU was associated with a significant inhibition of cell migration, proliferation and invasion, supporting the importance of hyaluronan synthesis in cancer, and the therapeutic potential of hyaluronan synthesis inhibition.     

Potential bias and mitigations when using stable isotope labeled parent drug as internal standard for LC-MS/MS quantitation of metabolites

In recent years, increasing emphasis has been placed on quantitative characterization of drug metabolites for better insight into the correlation between metabolite exposure and toxicological observations or pharmacological efficacy. One common strategy for metabolite quantitation is to adopt the stable isotope labeled (STIL) parent drug as the internal standard in an isotope dilution liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay. In the current work, we demonstrate this strategy could have a potential pitfall resulting in quantitation bias if the internal standard is subject to ion suppression from the co-eluting parent drug in the incurred samples. Propranolol and its metabolite 4-hydroxypropranolol were used as model compounds to demonstrate this phenomenon and to systematically evaluate different approaches to mitigate the issue, including atmospheric pressure chemical ionization (APCI) mode of ionization, increased internal standard concentration, quantitation without internal standard, the use of a structural analog as internal standard, and dilution of the samples. Case studies of metabolite quantitation in nonclinical and clinical studies in drug development were also included to demonstrate the importance of using an appropriate bioanalytical strategy for metabolite quantitation in the real world. We present that bias of metabolite concentrations could pose a potential for poor estimation of safety risk. A strategy for quantitation of metabolites in support of drug safety assessment is proposed.     

Determination of casopitant and its three major metabolites in dog and rat plasma by positive ion liquid chromatography/tandem mass spectrometry

A sensitive, selective and quantitative method for the simultaneous determination of casopitant, a potent and selective antagonist of the human Neurokinin 1 (NK-1) receptor, and its three major metabolites M12, M13 and M31 was developed and validated in dog and rat plasma. Acetonitrile containing stable labeled internal standards for the four analytes was used to precipitate proteins in plasma. Chromatographic separation was obtained using a reversed phase column with multiple reaction monitoring turboionspray positive ion detection. The lower and upper limits of quantification for casopitant and its metabolites were 15 and 15,000 ng/mL, using a 50 μL of dog or rat plasma aliquot, respectively. The inter-day precision (relative standard deviation) and accuracy (relative error) in dog plasma, derived from the analysis of validation samples at 5 concentrations, ranged from 4.1% to 10.0% and −10.8% to 8.7%, respectively, for casopitant and its 3 major metabolites. The intra-day precision (relative standard deviation) and accuracy (relative error) in rat plasma, derived from the analysis of validation samples at 5 concentrations, ranged from 3.9% to 6.6% and −9.6% to 8.3%, respectively, for casopitant and its three metabolites. All analytes were found to be stable in analytical solutions for at least 43 days at 4 °C, in dog and rat plasma at room temperature for at least 24 h, at the storage temperature of −20 °C for at least 6 months, and following the action of three freeze–thaw cycles from −20 °C to room temperature. All analytes were also found to be stable in processed extracts at 4 °C for at least 72 h. This assay proved to be accurate, precise, fast and was used to support long-term toxicology studies in dog and rat.     

Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research

Despite the fact that data deposition is not a generalised fact yet in the field of proteomics, several mass spectrometry (MS) based proteomics repositories are publicly available for the scientific community. The main existing resources are: the Global Proteome Machine Database (GPMDB), PeptideAtlas, the PRoteomics IDEntifications database (PRIDE), Tranche, and NCBI Peptidome. In this review the capabilities of each of these will be described, paying special attention to four key properties: data types stored, applicable data submission strategies, supported formats, and available data mining and visualization tools. Additionally, the data contents from model organisms will be enumerated for each resource. There are other valuable smaller and/or more specialized repositories but they will not be covered in this review. Finally, the concept behind the ProteomeXchange consortium, a collaborative effort among the main resources in the field, will be introduced.     

Mapping photoautotrophic metabolism with isotopically nonstationary (13)C flux analysis

Understanding in vivo regulation of photoautotrophic metabolism is important for identifying strategies to improve photosynthetic efficiency or re-route carbon fluxes to desirable end products. We have developed an approach to reconstruct comprehensive flux maps of photoautotrophic metabolism by computational analysis of dynamic isotope labeling measurements and have applied it to determine metabolic pathway fluxes in the cyanobacterium Synechocystis sp. PCC6803. Comparison to a theoretically predicted flux map revealed inefficiencies in photosynthesis due to oxidative pentose phosphate pathway and malic enzyme activity, despite negligible photorespiration. This approach has potential to fill important gaps in our understanding of how carbon and energy flows are systemically regulated in cyanobacteria, plants, and algae.