Post-Translationally Modified Proteoforms as Biomarkers: From Discovery to Clinical Use.

Recent advances in proteomics technologies provide tremendous opportunities for biomarker-related clinical applications; however, the distinctive characteristics of human biofluids such as the high dynamic range in protein abundances and extreme complexity of the proteomes present tremendous challenges. In this review we summarize recent advances in LC-MS-based proteomics profiling and its applications in clinical proteomics as well as discuss the major challenges associated with implementing these technologies for more effective candidate biomarker discovery. Developments in immunoaffinity depletion and various fractionation approaches in combination with substantial improvements in LC-MS platforms have enabled the plasma proteome to be profiled with considerably greater dynamic range of coverage, allowing many proteins at low ng/ml levels to be confidently identified. Despite these significant advances and efforts, major challenges associated with the dynamic range of measurements and extent of proteome coverage, confidence of peptide/protein identifications, quantitation accuracy, analysis throughput, and the robustness of present instrumentation must be addressed before a proteomics profiling platform suitable for efficient clinical applications can be routinely implemented.

We have identified several protein biomarkers of three Campylobacter jejuni strains (RM1221, RM1859, and RM3782) by proteomic techniques. The protein biomarkers identified are prominently observed in the time-of-flight mass spectra (TOF MS) of bacterial cell lysate supernatants ionized by matrix-assisted laser desorption/ionization (MALDI). The protein biomarkers identified were: DNA-binding protein HU, translation initiation factor IF-1, cytochrome c553, a transthyretin-like periplasmic protein, chaperonin GroES, thioredoxin Trx, and ribosomal proteins: L7/L12 (50S), L24 (50S), S16 (30S), L29 (50S), and S15 (30S), and conserved proteins similar to strain NCTC 11168 proteins Cj1164 and Cj1225. The protein biomarkers identified appear to represent high copy, intact proteins. The significant findings are as follows: (1) Biomarker mass shifts between these strains were due to amino acid substitutions of the primary polypeptide sequence and not due to changes in post-translational modifications (PTMs). (2) If present, a PTM of a protein biomarker appeared consistently for all three strains, which supported that the biomarker mass shifts observed between strains were not due to PTM variability. (3) The PTMs observed included N-terminal methionine (N-Met) cleavage as well as a number of other PTMs. (4) It was discovered that protein biomarkers of C. jejuni (as well as other thermophilic Campylobacters) appear to violate the N-Met cleavage rule of bacterial proteins, which predicts N-Met cleavage if the penultimate residue is threonine. Two protein biomarkers (HU and 30S ribosomal protein S16) that have a penultimate threonine residue do not show N-Met cleavage. In all other cases, the rule correctly predicted N-Met cleavage among the biomarkers analyzed. This exception to the N-Met cleavage rule has implications for the development of bioinformatics algorithms for protein/pathogen identification. (5) There were fewer biomarker mass shifts between strains RM1221 and RM1859 compared to strain RM3782. As the mass shifts were due to the frequency of amino acid substitutions (and thus underlying genetic variations), this suggested that strains RM1221 and RM1859 were phylogenetically closer to one another than to strain RM3782 (in addition, a protein biomarker prominent in the spectra of RM1221 and RM1859 was absent from the RM3782 spectrum due to a nonsense mutation in the gene of the biomarker). These observations were confirmed by a nitrate reduction test, which showed that RM1221 and RM1859 were C. jejuni subsp. jejuni whereas RM3782 was C. jejuni subsp. doylei. This result suggests that detection/identification of protein biomarkers by pattern recognition and/or bioinformatics algorithms may easily subspeciate bacterial microorganisms. (6) Finally, the number and variation of PTMs detected in this relatively small number of protein biomarkers suggest that bioinformatics algorithms for pathogen identification may need to incorporate many more possible PTMs than suggested previously in the literature.

Liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM) has widespread clinical use for detection of inborn errors of metabolism, therapeutic drug monitoring, and numerous other applications. This technique detects proteolytic peptides as surrogates for protein biomarker expression, mutation, and post-translational modification in individual clinical assays and in cancer research with highly multiplexed quantitation across biological pathways. LC-MRM for protein biomarkers must be translated from multiplexed research-grade panels to clinical use. LC-MRM panels provide the capability to quantify clinical biomarkers and emerging protein markers to establish the context of tumor phenotypes that provide highly relevant supporting information. An application to visualize and communicate targeted proteomics data will empower translational researchers to move protein biomarker panels from discovery to clinical use. Therefore, we have developed a web-based tool for targeted proteomics that provides pathway-level evaluations of key biological drivers (e.g., EGFR signaling), signature scores (representing phenotypes) (e.g., EMT), and the ability to quantify specific drug targets across a sample cohort. This tool represents a framework for integrating summary information, decision algorithms, and risk scores to support Physician-Interpretable Phenotypic Evaluation in R (PIPER) that can be reused or repurposed by other labs to communicate and interpret their own biomarker panels.

Post-translational modifications (PTMs) are chemical or physical changes to proteins that can alter structure/function relationships and thus influence catalysis, cell localization and interactions with other proteins and biomolecules. There are over 200 recognized PTMs, generating a vast scope for altering protein function and increasing the potential for complex regulatory cross-talk between diverse modifications. Protein phosphorylation is of major significance since 30-50% of all cellular proteins may be targeted1,2. Phosphorylation is a transient means of amplifying environmental signals to rapidly alter protein structure, interactions and ultimately, function.

Biologics such as monoclonal antibodies are much more complex than small-molecule drugs, which raises challenging questions for the development and regulatory evaluation of follow-on versions of such biopharmaceutical products (also known as biosimilars) and their clinical use once patent protection for the pioneering biologic has expired. With the recent introduction of regulatory pathways for follow-on versions of complex biologics, the role of analytical technologies in comparing biosimilars with the corresponding reference product is attracting substantial interest in establishing the development requirements for biosimilars. Here, we discuss the current state of the art in analytical technologies to assess three characteristics of protein biopharmaceuticals that regulatory authorities have identified as being important in development strategies for biosimilars: post-translational modifications, three-dimensional structures and protein aggregation.

Australian elapid snakes are among the most venomous in the world. Their venoms contain multiple components that target blood hemostasis, neuromuscular signaling, and the cardiovascular system. We describe here a comprehensive approach to separation and identification of the venom proteins from 18 of these snake species, representing nine genera. The venom protein components were separated by two-dimensional PAGE and identified using mass spectrometry and de novo peptide sequencing. The venoms are complex mixtures showing up to 200 protein spots varying in size from <7 to over 150 kDa and in pI from 3 to >10. These include many proteins identified previously in Australian snake venoms, homologs identified in other snake species, and some novel proteins. In many cases multiple trains of spots were typically observed in the higher molecular mass range (>20 kDa) (indicative of post-translational modification). Venom proteins and their post-translational modifications were characterized using specific antibodies, phosphoprotein- and glycoprotein-specific stains, enzymatic digestion, lectin binding, and antivenom reactivity. In the lower molecular weight range, several proteins were identified, but the predominant species were phospholipase A2 and alpha-neurotoxins, both represented by different sequence variants. The higher molecular weight range contained proteases, nucleotidases, oxidases, and homologs of mammalian coagulation factors. This information together with the identification of several novel proteins (metalloproteinases, vespryns, phospholipase A2 inhibitors, protein-disulfide isomerase, 5'-nucleotidases, cysteine-rich secreted proteins, C-type lectins, and acetylcholinesterases) aids in understanding the lethal mechanisms of elapid snake venoms and represents a valuable resource for future development of novel human therapeutics.

Post‐translational modification and phenotype

LC–MS/MS for protein and peptide quantification in clinical chemistry

In the past decades the clinical laboratory had made significant technological advances focused on clinical efficiency and efficacy. Responding to the demand of an increased efficiency in clinical laboratory diagnosis, there has been a recent trend towards a more decentralized diagnostic analysis near to the patients. The idea of this so-called point-of-care testing (POCT) is to bring the test immediately and in a convenient way to the patient. These devices have been developed to offer improvements in convenience, patient care and turnaround time. POCT systems should be fast, small, and simple to use while maintaining state-of-the-art performance features. The concept of POCT represents a fundamental shift in diagnostic testing where the objective is cost-effective, patient-focused testing at the site of diagnosis. In this chapter, the concept of POCT, as well the idea of Lab-on-a-Chip technology is discussed in the fields of diabetes care, including the use of glucometers, gestational diabetes, continuous blood glucose monitoring, multiparameter analysis, general clinical chemistry, and the modern diagnosis of acute myocardial infarction. Modern methods in hematology also make use of the Lab-on-a-Chip and POCT technology. Last, but not least, the clinical use and performance characteristics of these laboratory tests are discussed in this chapter. The authors conclude that POCT and Lab-on-a-Chip technologies provide a revolutionary diagnostic technology in improving patient outcomes.

Rapid progression of genetic engineering technology has accelerated the development and availability of protein-based biopharmaceuticals for clinical use. However, their unique and complex structures render them susceptible to a plethora of post-translational modifications (PTMs) as well as chemical degradative processes they may encounter in distinct in vivo environments. Among the more common degradative reactions that can impact the structure and function of therapeutic proteins are oxidation, proteolysis, phosphorylation, and deamidation. Several PTMs such as oxidation further render modified proteins vulnerable to aggregation or proteolytic degradation by enzymatic or non-enzymatic mechanisms (Torosantucci et al., Pharm Res 31(3):541–553, 2014). Degradation of a therapeutic protein in vivo becomes problematic when the structural modification alters its intended function and safety or efficacy profile (Foye, Lippincott Williams & Wilkins, Philadelphia, 2008). As a result of protein aggregation or degradation, therapeutic activity can be decreased, increased, or altered to have off-target effects. Protein degradation or aggregation could be facilitated under inflammatory circumstances in diverse clinical settings such as cancer, chronic inflammatory diseases, organ transplants, infectious diseases, and cardiovascular disorders, and can exacerbate an inflammatory response with unintended consequences (Chennamsetty et al., Proc Natl Acad Sci U S A 106(29):11937–11942, 2009; Hermeling et al., Pharm Res, 21(6):897–903, 2004). Therefore, characterizing and controlling the degradation or aggregation profiles for a therapeutic protein, especially for indications where the physiological environment presents additional opportunity for instability, is an essential component of a drug manufacturer’s control strategy. Evaluating a manufacturer’s control strategy is a key risk assessment tool for the regulation of investigational and licensed biologic drugs for human use. Better risk assessment can result from (1) greater characterization of critical structural modifications that can influence therapeutic protein function (2), application of sensitive and suitable methods to objectively measure protein modifications, and (3) use of relevant preclinical models or human tissue samples for predicting the in vivo impact of the inflammatory environment on such protein alterations. The increasing number of novel investigational drugs and the simultaneous demand for safer and more effective drugs warrants the need to examine the mechanisms by which therapeutic proteins are modified in vitro and in vivo, as well as apply modern analytical and genetic engineering techniques to design biobetter biologic drugs with improved safety and efficacy profiles. This chapter will examine factors known to alter the stability of therapeutic proteins in vivo, potential interactions of susceptible proteins with the inflammatory environment, and review some challenges and potential strategies for designing biobetters.

Over the last decade, genomics research in psychiatry and neuroscience has provided important insights into genes expressed under different physiological and pathophysiological conditions. Contrary to the great expectations regarding a clinical use of these datasets, genomics failed to improve markedly the diagnostic and therapeutic options in brain disorders. Due to alternative splicing and posttranslational modifications, one single gene determines a multitude of gene products. Therefore, in order to understand molecular processes in neuropsychiatric disorders, it is necessary to unravel signal transduction pathways and complex interaction networks on the level of proteins, not only DNA and mRNA. Proteomics utilises high-throughput mass spectrometric protein identification that can reveal protein expression levels, posttranslational modifications and protein-protein interactions. Proteomic tools have the power to identify quantitative and qualitative protein patterns in postmortem brain tissue, cerebrospinal fluid (CSF) or serum, thus increasing the knowledge about etiology and pathomechanisms of brain diseases. Comparing protein profiles in healthy and disease states provides an opportunity to establish specific diagnostic and prognostic biomarkers. In addition, proteomic studies of the effects of medication - in vitro and in vivo - might help to design specific pharmaceutical agents with fewer side effects. In this overview, we present the most widely used proteomic techniques and illustrate the potential and limitations of this field of research. Furthermore, we provide insight into the contributions of proteomics to the study of psychiatric diseases such as Alzheimer's disease, drug addiction, schizophrenia and depression.

Objective To investigate the clinical and radiological characteristics and laboratory diagnosis of pulmonary nocardiosis,to improve the recognization and decrease the misdiagnosis of this disease.Methods The clinical feature,radiological characteristics,laboratory diagnosis and treatment were reported in three cases of pulmonary nocardiosis with review of related literature.Results The disease was without specific clinical feature.A computer tomography scan of chest showed multiple cavitary nodules and lamellar high density shadow in both lungs,which was easily to misdiagnose.The most precise diagnosis could be provided by bacteriology examination.Conclusions Pulmonary nocardiosis is a rarely specific infection and the diagnosis is based on the bacteriology examination. Key words: Pneumonia; Nocardia; Diagnosis

During their biological life, proteins are exposed in a cumulative fashion to irreversible nonenzymatic, late posttranslational modifications that are responsible for their molecular aging. It is now well established that these damaged proteins constitute a molecular substratum for many dysfunctions described in metabolic and age-related diseases, such as diabetes mellitus, renal insufficiency, atherosclerosis, or neurodegenerative diseases. Accordingly, the specific end products derived from these reactions are considered potentially useful biomarkers for these diseases. The aim of this review is to give an overview of nonenzymatic posttranslational modifications of proteins and their influence in vivo, take inventory of the analytical methods available for the measurement of posttranslational modification-derived products, and assess the potential contribution of new technologies for their clinical use as biological markers of protein molecular aging. Despite their clinical relevance, biomarkers of posttranslational modifications of proteins have been studied only in the context of experimental clinical research, owing to the analytical complexity of their measurement. The recent implementation in clinical chemistry laboratories of mass spectrometry-based methods that provide higher specificity and sensitivity has facilitated the measurement of these compounds. These markers are not used currently by clinicians in routine practice, however, and many challenges, such as standardization, have to be confronted before these markers can be used as efficient tools in the detection and monitoring of long-term complications of metabolic and age-related diseases.

The major advances from research on platelet molecular and cell biology, physiology, and pathophysiology over the past decades have not been adequately translated to clinical laboratory diagnosis. Hereditary platelet function disorders (PFDs) are at least as prevalent in the general population as von Willebrand disease (VWD) although PFDs tend not be as well recognized or evaluated. Clinical mucous and skin bleeding in patients with PFDs is prototypic of primary hemostasis disorders, and the bleeding pattern is not distinguishable from that of other primary hemostasis disorders such as VWD. However, different treatment needs, between these discrete disorders, make a precise diagnosis mandatory. Currently, clinicians receive reliable laboratory reports when testing patients with severe PFDs, such as Glanzmann thrombasthenia and Bernard-Soulier syndrome, due to the distinctive laboratory defects that these disorders present, together with the availability of differential diagnostic tests. This is not the case for the majority of PFDs generically classified as "platelet secretion disorders," which are a heterogeneous group of "mild bleeding disorders," for which there are not universally accepted diagnostic criteria. An important reason for robust diagnostic tests is the high proportion (more than 50% in some reports) of patients with unequivocal bleeding who have no precise diagnosis established after a complete laboratory workup. It is paradoxical that the current "gold standard" test for PFD diagnosis, light transmission aggregometry (LTA), has not been standardized after more than four decades of worldwide clinical use. This review describes current diagnostic assays for PFD in a clinical hemostasis laboratory, relating these with current knowledge on platelet function and pathophysiology. Special emphasis will be given to LTA and platelet secretion tests, as well as to the reasons why sensitive tests are needed to explore the lesser known participation of platelets in blood clotting and fibrinolytic processes.

Considerations when using next-generation sequencing for genetic diagnosis of long-QT syndrome in the clinical testing laboratory