Advances in mass spectrometry-based cancer research and analysis: from cancer proteomics to clinical diagnostics

Introduction: The last 20 years have seen significant improvements in the analytical capabilities of biological mass spectrometry. Studies using advanced mass spectrometry (MS) have resulted in new insights into cell biology and the aetiology of diseases as well as its use in clinical applications. Areas Covered: This review will discuss recent developments in MS-based technologies and their cancer-related applications with a focus on proteomics. It will also discuss the issues around translating the research findings to the clinic and provide an outline of where the field is moving. Expert Opinion: Proteomics has been problematic to adapt for the clinical setting. However, MS-based techniques continue to demonstrate potential in novel clinical uses beyond classical cancer proteomics

Programmed cell death 6 interacting protein (PDCD6IP) and Rabenosyn-5 (ZFYVE20) are potential urinary biomarkers for upper gastrointestinal cancer

PURPOSE: Cancer of the upper digestive tract (uGI) is a major contributor to cancer-related death worldwide. Due to a rise in occurrence, together with poor survival rates and a lack of diagnostic or prognostic clinical assays, there is a clear need to establish molecular biomarkers. EXPERIMENTAL DESIGN: Initial assessment was performed on urine samples from 60 control and 60 uGI cancer patients using MS to establish a peak pattern or fingerprint model, which was validated by a further set of 59 samples. RESULTS: We detected 86 cluster peaks by MS above frequency and detection thresholds. Statistical testing and model building resulted in a peak profiling model of five relevant peaks with 88% overall sensitivity and 91% specificity, and overall correctness of 90%. High-resolution MS of 40 samples in the 2-10 kDa range resulted in 646 identified proteins, and pattern matching identified four of the five model peaks within significant parameters, namely programmed cell death 6 interacting protein (PDCD6IP/Alix/AIP1), Rabenosyn-5 (ZFYVE20), protein S100A8, and protein S100A9, of which the first two were validated by Western blotting. CONCLUSIONS AND CLINICAL RELEVANCE: We demonstrate that MS analysis of human urine can identify lead biomarker candidates in uGI cancers, which makes this technique potentially useful in defining and consolidating biomarker patterns for uGI cancer screening

Systems Biology Approaches to Disease Marker Discovery

Do razvoja integracijskih procesa u hotelijerstvu došlo je zbog uvjeta i utjecaja globalizacije koja je zahvatila svjetsko gospodarstvo, pa tako i hotelijerstvo. Tržište je jedan od glavnih faktora u ostvarivanju uspješnog poslovanja hotelskih poduzeća, koja se povezivanjem predstavljaju stranom tržištu kako bi povećala prodaju proizvoda i usluga te time pozitivno utjecala na sveukupno gospodarstvo države. Integracijski procesi su nužni i sve više prisutniji na svjetskom tržištu. U turizmu postoji više oblika integracijskih procesa. Najučestaliji oblik je horizontalni gdje se povezuju hoteli i nastaju veliki hotelski lanci. Kako se svjetski turizam sve više razvija i tržište se širi tako se povećava i konkurencija. Hotelska poduzeća povezuju se i vertikalno te se tako integriraju, primjerice: turoperatori i turističke agencije s avionskim poduzećima, spajaju se lanci hotela i turoperatori i tako dalje. Prednosti hotelskih grupacija omogućuju diversificiranje ponude proizvoda i usluga, širenje na svjetskom tržištu, povećavaju konkurentnost te postižu ekonomiju razmjera. Tako se privlače i potencijalni kupci, stoga rezultat integracija znači stvaranje više prihoda. Također, hotelske grupacije smanjuju ukupne troškove tehnologije, marketinga, proizvodnje i distribucije. Jedan od glavnih razloga povezivanja uključuje jačanje hotelske kompanije i brenda, pristup novim kanalima distribucije i povećavanje dobiti. Nadalje, prodajom svojih proizvoda i usluga potrošačima jamči se i efikasnost u procesu proizvodnje. Usprkos prednostima postoje i nedostaci koji prate integracijske procese, kao što su smanjena fleksibilnost jer su novonastale veće grupacije, zatim širenje kompanije znači potreba za većom transparentnošću, moguće prepreke prilikom ulaska u novo tržište, ograničavanje konkurencije i velika ulaganja koje prati i poslovni rizik. Hotelski sektor u Hrvatskoj bilježi visoku konsolidaciju. U Hrvatskoj se nalazi 5 glavnih hotelskih grupacija, a to su: Valamar hoteli i ljetovlišta, Maistra i Jadranski Luksuzni hoteli koji upravljaju s gotovo 50% ukupnih kapaciteta, zatim slijede Plava Laguna i Sunce koncern. Osim njih, najveće svjetske hotelske grupacije locirane su u turistički najrazvijenim gradovima u Hrvatskoj, primjerice Marriott International, a najviše ih se nalazi u Dubrovniku, Istri, Splitu i Zagrebu. Brendirani hoteli stvaraju prepoznatljivost Hrvatske na međunarodnom tržištu, pa tako i samu promociju destinacije. Nadalje, razlozi povezivanja svjetskih i domaćih grupacija omogućili su Hrvatskoj širenje i privlačenje potencijalnih gostiju, kvalitetniju prodaju proizvoda i usluga, povećavanje konkurentnosti, zapošljavanja, marketinga, kao i veću ekonomsku dobit te smanjenje troškova poslovanja.The development of integration processes in the hospitality industry was due to the conditions and the impact of globalization, which has engulfed the global economy, and so has the hospitality industry. The market is one of the main factors in the successful operation of hotel companies, which by connecting themselves represent the foreign market in order to increase the sale of products and services and thus have a positive impact on the overall economy of the country. Integration processes are necessary and increasingly present in the world market. There are several forms of integration processes in tourism. The most common form is horizontal where hotels connect and large hotel chains are formed. As world tourism grows more and the market expands, so does competition. Hotel companies also connect vertically to integrate, for example: tour operators and travel agencies with airlines, merging hotel chains and tour operators, and so on. Advantages of hotel groups enable diversification of product and service offerings, expansion in the world market, increase competitiveness and achieve economies of scale. This is how potential customers are attracted, so the result of integrations means generating more revenue. Also, hotel groups reduce the overall cost of technology, marketing, production and distribution. One of the main reasons for connectivity is to strengthen the hotel company and brand, access new distribution channels and increase profits. Furthermore, the sale of its products and services to consumers also guarantees efficiency in the production process. Despite the advantages, there are disadvantages that accompany integration processes, such as reduced flexibility because newer groups are emerging, then expanding the company means more transparency, possible barriers to entry, restriction of competition and large investments that accompany business risk. The hotel sector in Croatia is in high consolidation. There are 5 major hotel groups in Croatia, namely: Valamar hotels and resorts, Maistra and Adriatic Luxury Hotels, which manage almost 50% of the total capacity, followed by Blue Lagoon and Sun Concern. In addition, the world's largest hotel groups are located in the most developed tourist cities in Croatia, such as Marriott International, with the most hotels located in Dubrovnik, Istria, Split and Zagreb. The branded hotels create the recognition of Croatia on the international market, and thus the promotion of the destination itself. Furthermore, the reasons for connecting international and domestic groups have enabled Croatia to expand and attract potential guests, improve the quality of its products and services, increase competitiveness, employment, marketing, as well as greater economic profits and reduce operating costs

Salivary biomarker development using genomic, proteomic and metabolomic approaches.

The use of saliva as a diagnostic sample provides a non-invasive, cost-efficient method of sample collection for disease screening without the need for highly trained professionals. Saliva collection is far more practical and safe compared with invasive methods of sample collection, because of the infection risk from contaminated needles during, for example, blood sampling. Furthermore, the use of saliva could increase the availability of accurate diagnostics for remote and impoverished regions. However, the development of salivary diagnostics has required technical innovation to allow stabilization and detection of analytes in the complex molecular mixture that is saliva. The recent development of cost-effective room temperature analyte stabilization methods, nucleic acid pre-amplification techniques and direct saliva transcriptomic analysis have allowed accurate detection and quantification of transcripts found in saliva. Novel protein stabilization methods have also facilitated improved proteomic analyses. Although candidate biomarkers have been discovered using epigenetic, transcriptomic, proteomic and metabolomic approaches, transcriptomic analyses have so far achieved the most progress in terms of sensitivity and specificity, and progress towards clinical implementation. Here, we review recent developments in salivary diagnostics that have been accomplished using genomic, transcriptomic, proteomic and metabolomic approaches

Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset

Diabetes like many diseases and biological processes is not mono-causal. On the one hand multifactorial studies with complex experimental design are required for its comprehensive analysis. On the other hand, the data from these studies often include a substantial amount of redundancy such as proteins that are typically represented by a multitude of peptides. Coping simultaneously with both complexities (experimental and technological) makes data analysis a challenge for Bioinformatics

A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass

<p>Abstract</p> <p>Background</p> <p>Less than 25% of patients with a pelvic mass who are presented to a gynecologist will eventually be diagnosed with epithelial ovarian cancer. Since there is no reliable test to differentiate between different ovarian tumors, accurate classification could facilitate adequate referral to a gynecological oncologist, improving survival. The goal of our study was to assess the potential value of a SELDI-TOF-MS based classifier for discriminating between patients with a pelvic mass.</p> <p>Methods</p> <p>Our study design included a well-defined patient population, stringent protocols and an independent validation cohort. We compared serum samples of 53 ovarian cancer patients, 18 patients with tumors of low malignant potential, and 57 patients with a benign ovarian tumor on different ProteinChip arrays. In addition, from a subset of 84 patients, tumor tissues were collected and microdissection was used to isolate a pure and homogenous cell population.</p> <p>Results</p> <p>Diagonal Linear Discriminant Analysis (DLDA) and Support Vector Machine (SVM) classification on serum samples comparing cancer versus benign tumors, yielded models with a classification accuracy of 71-81% (cross-validation), and 73-81% on the independent validation set. Cancer and benign tissues could be classified with 95-99% accuracy using cross-validation. Tumors of low malignant potential showed protein expression patterns different from both benign and cancer tissues. Remarkably, none of the peaks differentially expressed in serum samples were found to be differentially expressed in the tissue lysates of those same groups.</p> <p>Conclusion</p> <p>Although SELDI-TOF-MS can produce reliable classification results in serum samples of ovarian cancer patients, it will not be applicable in routine patient care. On the other hand, protein profiling of microdissected tumor tissue may lead to a better understanding of oncogenesis and could still be a source of new serum biomarkers leading to novel methods for differentiating between different histological subtypes.</p

Characterization of Cell Glycocalyx with Mass Spectrometry Methods.

The cell membrane plays an important role in protecting the cell from its extracellular environment. As such, extensive work has been devoted to studying its structure and function. Crucial intercellular processes, such as signal transduction and immune protection, are mediated by cell surface glycosylation, which is comprised of large biomolecules, including glycoproteins and glycosphingolipids. Because perturbations in glycosylation could result in dysfunction of cells and are related to diseases, the analysis of surface glycosylation is critical for understanding pathogenic mechanisms and can further lead to biomarker discovery. Different mass spectrometry-based techniques have been developed for glycan analysis, ranging from highly specific, targeted approaches to more comprehensive profiling studies. In this review, we summarized the work conducted for extensive analysis of cell membrane glycosylation, particularly those employing liquid chromatography with mass spectrometry (LC-MS) in combination with various sample preparation techniques

Applications of Mass Spectrometry in Proteomics and Pharmacokinetics

Tremendous technology improvements of the last decades has given mass spectrometry a more and more expanding role in the study of a wide range of molecules: from the identification and quantification of small molecular weight molecules to the structural determination of biomacromolecules. Many are the fields of application for this technique and the various versions of it. In the present study three different applications have been explored. The first application is a pharmacokinetics study of anticancer drug Gemcitabine and its principal metabolite, where the role of the LC-MS/MS is essential both for the selectivity of the detection of the small analytes and the sensitivity enhanced by multi-reaction monitoring experiments. The design of the study involved the collection of several blood samples at selected times and from patients that would have met certain eligibility criteria. The ESI demonstrated to be the most suitable approach and it provided the necessary data to conclude that toxicity of Gemcitabine did not increase when administered at FDR (Fixed Dose Rate) infusion in patients with impaired hepatic function. The second application describes an example of how MS represents a powerful tool in cancer research, from serum profiling study with high resolution MALDITOF and bioinformatic analysis, to the identification of potential biomarker through peak identification. Almost 400 serum sample – homogeneously distributed between biopsy confirmed ovarian cancer and high risk serum samples – were analyzed on a high resolution MALDI-TOF instrument after automated reverse phase magnetic beads separation. The high throughput data have undergone sophisticated bioinformatic procedures that lead to a list of upand down-regulated peaks, although identification studies were possible only for those peaks that showed a good reproducibility. One down-regolated peak has been identified using the LC-MS/MS technique. The identified peak confirmed a basic role of fibrinogen in the ovarian cancer; the other four peaks that have been identified as down-regulated showed an absolutely not satisfactory ionization in electro-spray, therefore further analysis will be performed on these analytes in order to determinate their amino acidic sequence. The most suitable technique seems to be MALDI-TOF/TOF mass spectrometry, since the peptides already showed a good degree of ionization in MALDI. The third and last study belongs to a quite new field, which is the combination of immuno precipitation assays with MALDI-TOF (Immuno Precipitation Mass Spectrometry, IPMS) experiments in order to evaluate the specificity of a series of monoclonal antibodies to specific antigen. The automated assay that has been developed provides structural information about the antigen that binds the monoclonal antibody to be tested and previously conjugated to the surface of magnetic beads, ideal support for robotic automation. IPMS showed its potential as a complementary tool of crucial importance in the selection of the monoclonal antibody for the development of ELISA based assay to be applied in the screening of a consistent number of human specimens for the clinical validation of proteins indicated in literature as potential biomarkers. Mass spectrometry in association with fractionation techniques, such as liquid or magnetic beads chromatography, is a very flexible tool in the cancer research field. Further improvement in the instrumentation and in the technology will bring always more and more results to be confident in