Clinical applications of mass spectrometry-based proteomics in cancer: Where are we?

Tumor tissue processing methodologies in combination with data-independent acquisition mass spectrometry (DIA-MS) have emerged that can comprehensively analyze the proteome of multiple tumor samples accurately and reproducibly. Increasing recognition and adoption of these technologies has resulted in a tranche of studies providing novel insights into cancer classification systems, functional tumor biology, cancer biomarkers, treatment response and drug targets. Despite this, with some limited exceptions, MS-based proteomics has not yet been implemented in routine cancer clinical practice. Here, we summarize the use of DIA-MS in studies that may pave the way for future clinical cancer applications, and highlight the role of alternative MS technologies and multi-omic strategies. We discuss limitations and challenges of studies in this field to date and propose steps for integrating proteomic data into the cancer clinic.     

ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics

Background  

Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or MS^E) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer.     

A mass spectrometry-based method to screen for α-amidated peptides

Amidation is a post-translational modification found at the C-terminus of ~50% of all neuropeptide hormones. Cleavage of the C(α)-N bond of a C-terminal glycine yields the α-amidated peptide in a reaction catalyzed by peptidylglycine α-amidating monooxygenase (PAM). The mass of an α-amidated peptide decreases by 58 Da relative to its precursor. The amino acid sequences of an α-amidated peptide and its precursor differ only by the C-terminal glycine meaning that the peptides exhibit similar RP-HPLC properties and tandem mass spectral (MS/MS) fragmentation patterns. Growth of cultured cells in the presence of a PAM inhibitor ensured the coexistence of α-amidated peptides and their precursors. A strategy was developed for precursor and α-amidated peptide pairing (PAPP): LC-MS/MS data of peptide extracts were scanned for peptide pairs that differed by 58 Da in mass, but had similar RP-HPLC retention times. The resulting peptide pairs were validated by checking for similar fragmentation patterns in their MS/MS data prior to identification by database searching or manual interpretation. This approach significantly reduced the number of spectra requiring interpretation, decreasing the computing time required for database searching and enabling manual interpretation of unidentified spectra. Reported here are the α-amidated peptides identified from AtT-20 cells using the PAPP method.     

A new source of endothelial progenitor cells--vascular biology redefined?

The initial discovery of endothelial progenitor cells (EPCs) in tandem with emerging concepts in stem cell biology has generated enormous interest and excitement in fields as diverse as tissue engineering, regenerative medicine, and tumor and vascular biology. A recent paper by Ingram et al. identifies a complete hierarchy of EPCs in the vessel wall, providing a new framework for classification of cells supporting endopoiesis akin to that previously established for hematopoiesis. This could have fundamental implications for our understanding of the role of the endothelium and, more specifically, the role of EPC interfacing with the vessel wall in health and disease.     

A new series of macrolide derivatives with 4″-O-saccharide substituents

A series of novel derivatives of macrolide with 4″-O-mono- or disaccharides were synthesized. The corresponding glycosyl trichloroacetimidates were used as the donors in the glycosylations. The in vitro antibacterial activities of 7a–f and 13–16 against a panel of susceptible and resistant pathogens were tested. The modification of 4′′-O-mono- or disaccharides may lead to the understanding of interaction of the macrolide and the bacterial ribosome.     

IPN unit bank biology—a new type of biology curriculum

Abstract

IPN (Institut für die Pädagogik der Naturwissenschaften/Institute for Science Education) in Kiel has developed single curriculum units since 1969 showing that certain innovative aims, methods, media, and content of biology teaching are practicable in schools. These units are being published now as a flexible ‘unit bank’ which can either be adopted as a whole or the individual units, or parts thereof, fitted into existing syllabuses.     

A rapid MALDI-TOF mass spectrometry-based method for colistin susceptibility testing in Escherichia coli

Colistin is recognized as a last-resort treatment option against multi-drug resistant bacteria including carbapenem-resistant Enterobacteriaceae (CRE). However, the plasmid-mediated colistin-resistance gene mcr-1 has been reported globally resulting in an increase of colistin-resistant bacteria. A quick and accurate method for determining the pathogen resistance of colistin is therefore crucial in the clinic. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a potential tool forto be applied for antimicrobial susceptibility testing. We compared the growth of Escherichia coli strains in the presence or absence of colistin. Automated analyses of the spectra were performed with a prototype software tool written with package R. Three mcr-1-positive and six mcr-1-negative E. coli were used for establishing the model to obtain the optimal incubation time, the breakpoint concentration of colistin and cut-off of the relative growth (RG) value. The distinction between susceptible and resistant strains was already noticeable after 2 h of incubation. The best separation between the susceptible and resistant strains was achieved at a concentration of 4 µg ml^-1 and a relative growth cut-off value of 0.6. Application of the model for the analysis of 128 E. coli isolates, a sensitivity of 97.4% and a specificity of 88.2% were achieved compared with colistin MIC results. The rapid MALDI-TOF MS-based method approach is simple to set-up, uses a short incubation time, and had excellent outcomes with respect to sensitivity and specificity for colistin sensitivity testing in Escherichia coli.     

Liquid chromatography–mass spectrometry-based metabolomics for authenticity assessment of fruit juices

High performance liquid chromatography?Cmass spectrometry (HPLC?CMS) technique, employing a hybrid triple quadrupole/linear ion trap (QqQ/LIT) mass analyzer, was used for comprehensive metabolomic fingerprinting of several fruit juices types, prepared from expensive (orange) or relatively low-priced (apple, grapefruit) fruits. Following the automated data mining and pre-treatment step, the suitability of the multivariate HPLC?CMS metabolomic data for authentication, i.e., classification of fruit juice and adulteration detection, was assessed with the use of advanced chemometric tools (principal component analysis, PCA, and linear discrimination analysis, LDA). The LDA classification model, constructed and validated employing a highly variable samples set, was able to reliably detect 15% addition of apple or grapefruit juice to orange juice. In the final stage of this study, high performance liquid chromatography?Cquadrupole?Cquadrupole-time-of-flight mass spectrometry (HPLC?CQqTOFMS) measurements were performed in order to obtain data for identification of pre-selected marker compounds using elemental formula calculation and online databases search.     

Efficacy and safety of the ��mother��s kiss�� technique: a systematic review of case reports and case series

Background:

Foreign bodies lodged in the nasal cavity are a common problem in children, and their removal can be challenging. The published studies relating to the “mother’s kiss” all take the form of case reports and case series. We sought to assess the efficacy and safety of this technique.

Methods:

We performed a comprehensive search of the Cochrane library, MEDLINE, CINAHL, Embase, AMED Complementary and Allied Medicine and the British Nursing Index for relevant articles. We restricted the results to only those studies involving humans. In addition, we checked the references of relevant studies to identify further possibly relevant studies. We also checked current controlled trials registers and the World Health Organization search portal. Our primary outcome measures were the successful extraction of the foreign object from the nasal cavity and any reported adverse effects. We assessed the included studies for factors that might predict the chance of success of the technique. We assessed the validity of each study using the Newcastle–Ottawa scale.

Results:

Eight relevant published articles met our inclusion criteria. The overall success rate for all of the case series was 59.9% (91/152). No adverse effects were reported.

Interpretation:

Evidence from case reports and case series suggests that the mother’s kiss technique is a useful and safe first-line option for the removal of foreign bodies from the nasal cavities of children.Nasal foreign bodies are a common problem in children, most frequently occurring between the ages of 2 and 5 years, and their removal can be challenging.^1,2 Children in this age group have a natural fear of the unknown, and providing care to them can be difficult, especially if previous attempts to remove the foreign body have been painful.Potential complications, most notably the risk of aspiration of the foreign body, mean that objects should be removed from the nasal cavity in a timely fashion. Various techniques have been described: instrumental extraction (using a hook or nasal forceps), suction, balloon catheters,³ cyanoacrylate glue⁴ and various positive-pressure techniques, the simplest of which is to ask the child to blow his or her nose while occluding the unaffected nostril. However, this technique is only possible for older children.⁵ Alternatively, a bag valve mask can be applied over the child’s face, the bag then squeezed to apply a puff of air into the child’s mouth;⁶ a male–male tube adaptor can be attached to an oxygen or air outlet via oxygen tubing placed in the unaffected nostril;⁷ or the “mother’s kiss” or “parent’s kiss” technique can be used.The mother’s kiss was first described in 1965 by Vladimir Ctibor, a general practitioner from New Jersey.⁸ The mother, or other trusted adult, places her mouth over the child’s open mouth, forming a firm seal as if about to perform mouth-to-mouth resuscitation. While occluding the unaffected nostril with a finger, the adult then blows until they feel the resistance caused by closure of the child’s glottis, at which point the adult gives a sharp exhalation to deliver a short puff of air into the child’s mouth. This puff of air passes through the nasopharynx, out through the unoccluded nostril and, if successful, results in the expulsion of the foreign body. The procedure is fully explained to the adult before starting, and the child is told that the parent will give him or her a “big kiss” so that minimal distress is caused to the child. The procedure can be repeated a number of times if not initially successful. A modified mother’s kiss technique has been described,⁹ which involves the adult blowing into a straw in the child’s mouth. We did not include this technique in our review.Although the mother’s kiss technique has been sporadically mentioned in the literature in case reports and case series, it has yet to gain widespread acceptance. It is not a suitable intervention for evaluation using a randomized controlled trial, because there is no appropriate control group: nontreatment is unacceptable, and there is no gold standard for comparison.Randomized controlled trials are considered to be the best trial design, but some treatments result in a dramatic effect that may not require randomized trials.¹⁰ The mother’s kiss technique falls into this category, because the foreign body will not usually move without intervention. Hence, case reports are sufficient to show that the technique sometimes works. However, a systematic review is needed to clarify how often it works and under what circumstances.We sought to examine the existing evidence for the efficacy and safety of the mother’s kiss technique, to help clinicians understand this evidence and to confirm or refute the appropriateness of current practice.Although systematic reviews of randomized controlled clinical trials are now common, it is rare to see a report of a systematic review of case reports or case series, and the methods for performing such a review are less clearly defined and tested. The principal elements of a systematic review are the location, appraisal and synthesis of individual studies; however, there are pitfalls to traditional systematic reviews of clinical trials that can introduce bias and inaccuracy in the results, which must be avoided. For this systematic review of case reports and case series, we were ever mindful of the rationale behind the stages in systematic reviews of clinical trials and endeavoured to apply the same principles to reduce bias and improve accuracy.     

Epigenetics: A key regulator of platyhelminth developmental biology?

The Platyhelminthes (flukes/flatworms) are a large group of derived metazoans beautifully adapted for existence in diversely challenging ecosystems. As tractable examples of development and self-regeneration or as causative agents of aquacultural, veterinary and biomedically-relevant parasitic diseases, the platyhelminths are subject to intensive inter-disciplinary research. Given the complex lifestyles exhibited by individuals within this phylum, we postulate that epigenetic processes feature in many aspects of platyhelminth lifecycle diversity, development and environmentally-driven adaptations.     

Molecular mechanisms of acetylcholine receptor–lipid interactions: from model membranes to human biology

Lipids are potent modulators of the Torpedo nicotinic acetylcholine receptor. Lipids influence nicotinic receptor function by allosteric mechanisms, stabilizing varying proportions of pre-existing resting, open, desensitized, and uncoupled conformations. Recent structures reveal that lipids could alter function by modulating transmembrane α-helix/α-helix packing, which in turn could alter the conformation of the allosteric interface that links the agonist-binding and transmembrane pore domains—this interface is essential in the coupling of agonist binding to channel gating. We discuss potential mechanisms by which lipids stabilize different conformational states in the context of the hypothesis that lipid–nicotinic receptor interactions modulate receptor function at biological synapses.     

A new look at adipocyte lipid droplets: towards a role in the sensing of triacylglycerol stores?

Lipid droplets have been considered for a long time as inert intracytoplasmic deposits formed within cells under various conditions. Recently, new tools and new approaches have been used to visualize and study these intracellular structures. This revealed new aspects of lipid droplets biology and pointed out their organized structure and dynamic composition. In adipocytes, the specialized cell type for the storage of energy as fat, lipid droplets are particularly well-developed organelles, and exhibit unique properties. Also discussed in this paper is the view that lipid droplets, through specific candidate constituents, can play a role in the sensing of the level of their lipid stores by adipocytes.     

What is targeted proteomics? A concise revision of targeted acquisition and targeted data analysis in mass spectrometry

Targeted proteomics has gained significant popularity in mass spectrometry‐based protein quantification as a method to detect proteins of interest with high sensitivity, quantitative accuracy and reproducibility. However, with the emergence of a wide variety of targeted proteomics methods, some of them with high‐throughput capabilities, it is easy to overlook the essence of each method and to determine what makes each of them a targeted proteomics method. In this viewpoint, we revisit the main targeted proteomics methods and classify them in four categories differentiating those methods that perform targeted data acquisition from targeted data analysis, and those methods that are based on peptide ion data (MS1 targeted methods) from those that rely on the peptide fragments (MS2 targeted methods).     

Molecular biology of Ri-plasmid—A review

Agrobacterium rhizogenes transfers a segment of its plasmid to the plant genome. The transferred DNA contains genes which are involved in the synthesis of plant hormones. These genes express in the plant cell and give rise to rooty-tumors at the infection site. Transgenic plants can be readily regenerated from the rooty-tumors and the transferred DNA is transmitted to progeny plants. High regeneration potential and sustained maintenance of transferred DNA makes the bacterium a suitable vector for plant genetic engineering. DNA sequences homologous to the transferred DNA ofAgrobacterium rhizogenes were detected in some untransformed plant species suggesting a past infection byAgrobacterium rhizogenes during evolution of some genera, notably Nicotiana.