Translational proteomics: developing a predictive capacity -- a review

Mass spectrometry based translational proteomics for biomarker discovery and application in colorectal cancer

Colorectal cancer (CRC) is a leading cause of cancer-related death in the world. Clinically, early detection of the disease is the most effective approach to tackle this tough challenge. Discovery and development of reliable and effective diagnostic tools for the assessment of prognosis and prediction of response to drug therapy are urgently needed for personalized therapies and better treatment outcomes. Among many ongoing efforts in search for potential CRC biomarkers, MS-based translational proteomics provides a unique opportunity for the discovery and application of protein biomarkers toward better CRC early detection and treatment. This review updates most recent studies that use preclinical models and clinical materials for the identification of CRC-related protein markers. Some new advances in the development of CRC protein markers such as CRC stem cell related protein markers, SRM/MRM-MS and MS cytometry approaches are also discussed in order to address future directions and challenges from bench translational research to bedside clinical application of CRC biomarkers.

Predicting Preterm Labour: Current Status and Future Prospects

Preterm labour and birth are a major cause of perinatal morbidity and mortality. Despite modern advances in obstetric and neonatal management, the rate of preterm birth in the developed world is increasing. Yet even though numerous risk factors associated with preterm birth have been identified, the ability to accurately predict when labour will occur remains elusive, whether it is at a term or preterm gestation. In the latter case, this is likely due to the multifactorial aetiology of preterm labour wherein women may display different clinical presentations that lead to preterm birth. The discovery of novel biomarkers that could reliably identify women who will subsequently deliver preterm may allow for timely medical intervention and targeted therapeutic treatments aimed at improving maternal and fetal outcomes. Various body fluids including amniotic fluid, urine, saliva, blood (serum/plasma), and cervicovaginal fluid all provide a rich protein source of putative biochemical markers that may be causative or reflective of the various pathophysiological disorders of pregnancy, including preterm labour. This short review will highlight recent advances in the field of biomarker discovery and the utility of single and multiple biomarkers for the prediction of preterm birth in the absence of intra-amniotic infection.

Endobiogeny: a global approach to systems biology (part 1 of 2)

Endobiogeny is a global systems approach to human biology that may offer an advancement in clinical medicine based in scientific principles of rigor and experimentation and the humanistic principles of individualization of care and alleviation of suffering with minimization of harm. Endobiogeny is neither a movement away from modern science nor an uncritical embracing of pre-rational methods of inquiry but a synthesis of quantitative and qualitative relationships reflected in a systems-approach to life and based on new mathematical paradigms of pattern recognition.

Gestational diabetes mellitus: a positive predictor of type 2 diabetes?

The aim of this paper is to consider the relative benefits of screening for type two diabetes mellitus in women with a previous pregnancy complicated by gestational diabetes mellitus. Recent studies suggest that women who experience GDM are at a greater risk of developing type 2 diabetes within 10-20 years of their index pregnancy. If considered as a stand-alone indicator of the risk of developing type 2 diabetes, GDM is a poor diagnostic test. Most women do not develop GDM during pregnancy and of those that do most do not develop type 2 diabetes. There is, however, a clear need for better early detection of predisposition to disease and/or disease onset to significantly impact on this global pandemic. The putative benefits of multivariate approaches and first trimester and preconception screening to increase the sensitivity of risk assignment modalities for type 2 diabetes are proposed.

Translational plant proteomics: a perspective

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics.

Placental proteomics: a shortcut to biological insight

Proteomics analysis of biological samples has the potential to identify novel protein expression patterns and/or changes in protein expression patterns in different developmental or disease states. An important component of successful proteomics research, at least in its present form, is to reduce the complexity of the sample if it is derived from cells or tissues. One method to simplify complex tissues is to focus on a specific, highly purified sub-proteome. Using this approach we have developed methods to prepare highly enriched fractions of the apical plasma membrane of the syncytiotrophoblast. Through proteomics analysis of this fraction we have identified over five hundred proteins several of which were previously not known to reside in the syncytiotrophoblast. Herein, we focus on two of these, dysferlin and myoferlin. These proteins, largely known from studies of skeletal muscle, may not have been found in the human placenta were it not for discovery-based proteomics analysis. This new knowledge, acquired through a discovery-driven approach, can now be applied for the generation of hypothesis-based experimentation. Thus discovery-based and hypothesis-based research are complimentary approaches that when coupled together can hasten scientific discoveries.

Proteomics of the human placenta: promises and realities

Proteomics is an area of study that sets as its ultimate goal the global analysis of all of the proteins expressed in a biological system of interest. However, technical limitations currently hamper proteome-wide analyses of complex systems. In a more practical sense, a desired outcome of proteomics research is the translation of large protein data sets into formats that provide meaningful information regarding clinical conditions (e.g., biomarkers to serve as diagnostic and/or prognostic indicators of disease). Herein, we discuss placental proteomics by describing existing studies, pointing out their strengths and weaknesses. In so doing, we strive to inform investigators interested in this area of research about the current gap between hyperbolic promises and realities. Additionally, we discuss the utility of proteomics in discovery-based research, particularly as regards the capacity to unearth novel insights into placental biology. Importantly, when considering under studied systems such as the human placenta and diseases associated with abnormalities in placental function, proteomics can serve as a robust 'shortcut' to obtaining information unlikely to be garnered using traditional approaches.

Antibody-based Proteomics: From bench to bedside

Over the past 75 years, antibodies have gone from being recognized as disease biomarkers to being used as very powerful therapeutic tools. This evolution has been accelerated by the identification of mAb and the extensive use of immunological tools both at fundamental and clinical levels. In this review, we evaluate how antibodies can be used to assess the proteome of cells or tissues and their relevance for clinical applications. These antibody-based proteomics approaches also require analytical and technological pipelines as well as specific enabling tools which are described. Our first objective was to establish how large-scale datasets (provided by high-throughput studies such as proteomics and transcriptomics) can be integrated with literature searches and clinical data to identify potentially relevant markers against which antibodies should be raised. Then based on an extensive literature review and our experience, we compare the methodologies developed to produce specific antibodies either in vivo or in vitro. This is followed by the description of the validation tools currently available and it also includes the use of antibody-based approaches in the establishment of molecular signatures utilized at the bench and soon available for bedside use.

Antibody microarray-based oncoproteomics

The driving force behind oncoproteomics is the belief that certain protein signatures or patterns exist that are associated with a particular malignancy. If so, the correlation of clinical parameters with defined protein expression patterns would allow us to predict disease progression and perhaps even postulate improved therapeutic modalities. The technological challenges to achieve these goals are significant, as the human proteome is not defined. No general methodological approach exists today, and human cancer can, furthermore, be divided into several disease subgroups. One potential solution to finding cancer-associated protein signatures is the emerging technology of affinity proteomics. This approach addresses some of the shortcomings of traditional proteomics and combines it with the power of microarrays. The present review focuses on the role of antibody microarrays in oncoproteomics and its potential to provide a truly proteome-wide analytical approach.