Implementation of Proteomics in Clinical Trials

The application of protein (or peptide) biomarkers in clinical studies is a dynamic, ever‐growing field. The introduction of clinical proteomics/peptidomics, such as mass spectrometry–based assays and multiplexed antibody–based protein arrays, has reshaped the landscape of biomarker identification and validation, allowing the discovery of novel biomarkers at an unprecedented rate and reliability. To reflect the current status with respect to implementation of protein/peptide biomarkers, an investigation of the most recent (last 6 years) clinical studies from clinicaltrials.gov is presented. Forty‐two clinical trials involving the direct use of protein or peptide biomarkers in patient stratification and/or disease diagnosis and prognosis are highlighted. Most of the clinical trials that include proteomics/protein assays are aiming toward implementation of non‐invasive diagnostic tools for early detection, while many of the clinical trials are targeting to correlate the protein abundance with the risk of a disease event. Less in number are the studies in which the protein biomarkers are applied to stratify the patients for intervention. All the above areas of application are considered of great importance for improving disease management, in an era where implementation toward precision medicine is the desired outcome of proteomics biomarker research.     

Implementation of Clinical Proteomics: A Step Closer to Personalized Medicine?

The success of clinical proteomics, per definition, is ultimately defined by the clinical implementation of proteomics findings. Extensive research activity in the field, targeting especially biomarker discovery, has been conducted in the past decades, with several studies suggesting a benefit from proteome‐based application in patient management. This viewpoint article discusses the current status in clinical proteomics with respect to implementation (as evidenced by the use of protein findings in drug labeling and patient stratification), and proposes specific action points for accelerating the biomarker validation process, placing special emphasis on the importance of data and resource sharing.     

The long path towards implementation of clinical proteomics: Exemplified based on CKD273

Clinical proteomics aims at the development and the implementation of novel biomarkers that demonstrate a clear clinical benefit in the management of diseases. However, though the attention in the field is increasing and multiple articles on biomarker research are published, clinical implementation of these biomarkers is scarce. In this paper, we aim towards identifying the hurdles on the path towards implementation, and present one successful approach, based on capillary electrophoresis coupled with mass spectrometry. A panel of biomarkers identified and assessed using this approach, termed CKD273, has recently received a Letter‐of‐Support from the US‐Food and Drug Administration (FDA), and is now implemented in the (early) management of chronic kidney disease. Based on this experience in the process towards implementation of CKD273, issues associated with implementation and suggestions how to meet these challenges are given.     

Urinary Proteomics and Precision Medicine for Chronic Kidney Disease: Current Status and Future Perspectives

Precision medicine is since long an ongoing refinement of classical medicine, integrating improved and more detailed pathophysiological understanding with rapid technological advances. In the heterogenous area of chronic kidney disease there seems to be a high potential for the improvement in treatment and prognosis for several causes, with new technologies under development, that are yet to be introduced in clinical practice. As in other medical disciplines, investigation of abundant peptide patterns (proteomics) has gained recent interest. Especially relevant for kidney disease, urinary proteomics may provide both improved diagnosis and, as reviewed here, also holds promise for personalized treatment in the future. So far, capillary electrophoresis coupled to mass spectrometry (CE‐MS) is the most widely applied technique, and in addition to several cross‐sectional and cohort studies, there is even an ongoing randomized controlled trial that will soon report on the concept used as a method of personalizing treatment. In addition, there is hope that urinary proteomics can turn into a “liquid biopsy,” replacing the invasive diagnostic procedure. The next couple of years will provide more answers on the topic.     

Urinary proteomics in cardiovascular disease: Achievements, limits and hopes

Cardiovascular disease (CVD) is the major cause of mortality and morbidity worldwide. Diagnosis of CVD and risk stratification of patients with CVD remains challenging despite the availability of a wealth of non-invasive and invasive tests. Clinical proteomics analyses a large number of peptides and proteins in biofluids. For clinical applications, the urinary proteome appears particularly attractive due to the relative low complexity compared with the plasma proteome and the noninvasive collection of urine. In this article, we review the results from pilot studies into urinary proteomics of coronary artery disease and discuss the potential of urinary proteomics in the context of pathogenesis of CVD.     

High-resolution biomarker discovery: Moving from large-scale proteome profiling to quantitative validation of lead candidates

Diverse proteomic techniques based on protein MS have been introduced to systematically characterize protein perturbations associated with disease. Progress in clinical proteomics is essential for personalized medicine, wherein treatments will be tailored to individual needs based on patient stratification using noninvasive disease monitoring procedures to reveal the most appropriate therapeutic targets. However, breakthroughs await the successful development and application of a robust proteomic pipeline capable of identifying and rigorously assessing the relevance of multiple candidate proteins as informative diagnostic and prognostic indicators or suitable drug targets involved in a pathological process. While steady progress has been made toward more comprehensive proteome profiling, the emphasis must now shift from in depth screening of reference samples to stringent quantitative validation of selected lead candidates in a broader clinical context. Here, we present an overview of the emerging proteomic strategies for high-throughput protein detection focused primarily on targeted MS/MS as the basis for biomarker verification in large clinical cohorts. We discuss the conceptual promise and practical pitfalls of these methods in terms of achieving higher dynamic range, higher throughput, and more reliable quantification, highlighting research avenues that merit additional inquiry.     

慢性肾脏病分期及短信提醒系统

根据医院肾病科的需求,设计并实现基于B/S三层体系结构的慢性肾脏病分期及短信提醒系统。该系统对慢性肾脏病患者按肾小球滤过率（GFR）进行分级管理,以发送手机短信的方式,为不同级别患者发送相应的治疗和护理等指导信息,帮助患者更好地控制和治疗疾病。本文从系统需求分析、体系架构、系统业务流程、数据库的设计及系统实现中的关键技术等方面介绍慢性肾脏病分期及短信提醒系统的设计与实现。目前,系统正在试运行阶段,如果使用效果良好,可以推广到其他慢性病的防治中去,意义重大。      

Application of proteomic techniques to the study of urine and renal tissue

The increasing application of proteomic methods to biomedical research is providing us with important new information; it holds particular promise in advancing basic and clinical renal research, but whether proteomics can ever become a routine diagnostic tool in nephrology is still uncertain. Currently, proteomic techniques are used by many groups in the search for "biomarkers" of disease, especially kidney disease, because of the ready availability of urine as an "end-product" of renal function. However, the question as to whether any disease-specific biomarkers exist or can be identified by proteomics is also uncertain. A growing application of proteomics in biomedical research is to understand the mechanism(s) of disease. This brief review is selective; in it we consider examples of proteomic studies of human urine for biomarkers, others that have explored renal physiology, and still others that have begun to probe the proteome of organelles. No single approach is sufficiently comprehensive, and the pooled application of proteomics to renal research will undoubtedly improve our understanding of renal function and enable us to explore in more detail subcellular structures, and to characterize cellular processes at the molecular level. When combined with other techniques in renal research, proteomics, and related analytical methods could prove indispensable in modeling renal function, and perhaps also in diagnosis and management of renal disease.     

Proteomic and other mass spectrometry based “omics” biomarker discovery and validation in pediatric venous thromboembolism and arterial ischemic stroke: Current state,unmet needs,and future directions

Venous thromboembolism (VTE) and arterial ischemic stroke (AIS) are increasingly-recognized health conditions in children, with both acute and chronic sequelae. Risk factors for, and pathogenesis of, VTE are readily related to three principal factors, consisting of venous stasis, endothelial damage, and the hypercoagulable state (i.e. thrombophilia), termed the triad of Virchow. In children, greater than 90% of VTE are provoked by an overt clinical risk factor, the most common of which is a central venous catheter. Risk factors for childhood-onset (beyond the neonatal period) AIS include sickle cell disease, infection, cerebral arteriopathy, and congenital cardiac disease. In perinatal AIS, risk factors are less well-defined, and have been hypothesized to include maternal-fetal conditions. While some acquired and inherited thrombophilias have been associated with increased risk of incident and/or recurrent VTE and AIS, knowledge of other diagnostic and prognostic biomarkers of VTE/AIS in children remains quite limited. To date, very few published studies have employed plasma mass spectrometry-based “omics” approaches (proteomics, lipidomics or metabolomics). Ongoing and future research efforts involving multicenter prospective study-derived plasma biobanks in pediatric VTE (such as the Kids-DOTT trial) and AIS (including VIPS) along with new multi-omics-compatible sample processing methods offer fertile opportunities for discovery and validation of both novel risk factors and prognostic markers, with great potential to achieve improved prognostic stratification in these diseases.     

Profiling the proteome in renal transplantation

Improved monitoring of transplanted solid organs is one of the next crucial steps leading to an increase in both patient and allograft survival. This can be facilitated through one or a set of surrogate biomarker molecules that accurately and precisely indicate the health status of the transplanted organ. Recent developments in the field of high throughput "omic" methods including genomics and proteomics have facilitated robust and comprehensive analysis of genes and proteins. This development has stimulated efforts in the identification of effective and clinically applicable gene and protein biomarkers in solid organ transplantation, including kidney transplantation. Some achievements have been made through proteomics in terms of profiling proteins and identification of potential biomarkers. However, the road to a successful biomarker discovery and its clinical implementation has proved to be challenging, requiring a number of key issues to be addressed. Such issues are: the lack of widely accepted protocols, difficulty in sample processing and transportation and a lack of collaborative efforts to achieve significant sample sizes in clinical studies. In this review using our area of expertise, we describe the current strategies used for proteomic-based biomarker discovery in renal transplantation, discuss inherent issues associated with these efforts and propose better strategies for successful biomarker discovery.     

慢性肾病辅助诊断系统的设计与实现

针对慢性肾病在全球占比之高、病情发展不可逆转、病情极易出现恶化的特点,设计了慢性肾病辅助诊断系统。利用数据挖掘随机森林算法的分类功能对病人化验数据进行处理,判断病人是否患有慢性肾病。设计并开发了基于B/S的慢性肾病辅助诊断系统,该系统集慢性肾病辅助诊断、诊断信息查看、用户管理于一体。该系统用于给经验不足的医生提供诊断参考,助其提高诊断水平,降低误诊率,从而使慢性肾病患者尽早进行正确的治疗,避免病情治疗延误带来的严重后果。     

Using data-independent,high-resolution mass spectrometry in protein biomarker research: Perspectives and clinical applications

In medicine, there is an urgent need for protein biomarkers in a range of applications that includes diagnostics, disease stratification, and therapeutic decisions. One of the main technologies to address this need is MS, used for protein biomarker discovery and, increasingly, also for protein biomarker validation. Currently, data-dependent analysis (also referred to as shotgun proteomics) and targeted MS, exemplified by SRM, are the most frequently used mass spectrometric methods. Recently developed data-independent acquisition techniques combine the strength of shotgun and targeted proteomics, while avoiding some of the limitations of the respective methods. They provide high-throughput, accurate quantification, and reproducible measurements within a single experimental setup. Here, we describe and review data-independent acquisition strategies and their recent use in clinically oriented studies. In addition, we also provide a detailed guide for the implementation of SWATH-MS (where SWATH is sequential window acquisition of all theoretical mass spectra)—one of the data-independent strategies that have gained wide application of late.     

Vascular proteomics and the discovery process of clinical biomarkers: The case of TWEAK

In the last years, big efforts are devoted to the search of novel biomarkers. Proteomic approaches in healthy and pathological samples may help us to discern differential protein expression patterns. These identified proteins include potential culprits in pathological pathways and/or clinical biomarkers to identify individuals at risk. However, extensively validation must be carried out before their implementation into the clinical practice. Biomarkers need to discriminate between health and disease, detect preclinical disease stages, have impact on survival prediction, and add predictive value beyond traditional risk factors and global risk algorithms. Now, we summarize the data of soluble tumor necrosis factor-like weak inducer of apoptosis (sTWEAK), a new cardiovascular biomarker identified by proteomic analysis. Decreased sTWEAK concentrations have been shown in patients with carotid atherosclerosis, coronary artery disease, congestive heart failure, peripheral artery disease, or chronic kidney disease (CKD). sTWEAK predicted adverse outcomes in patients with heart failure, myocardial infarction, and CKD. Finally, different drug regimens were able to modify sTWEAK plasma levels in patients with CKD. Although sTWEAK seems so far to fulfill the requisites in the development of a new biomarker, more large-scale studies are warranted to consolidate its usefulness.     

Cardiovascular proteomics: translational studies to develop novel biomarkers in heart failure and left ventricular remodeling

Heart failure (HF) remains a severe disease with a poor prognosis. HF biomarkers may include demographic features, cardiac imaging, or genetic polymorphisms but this term is commonly applied to circulating serum or plasma analytes. Biomarkers may have at least three clinical uses in the context of HF: diagnosis, risk stratification, and guidance in the selection of therapy. Proteomic studies on HF biomarkers can be designed as case/control using clinical endpoints; alternatively, left ventricular remodeling can be used as a surrogate endpoint. The type of samples (tissue, cells, serum or plasma) used for proteomic analysis is a key factor in the research of biomarkers. Since the final aim is the discovery of circulating biomarkers, and since plasma and serum samples are easily accessible, proteomic analysis is frequently used for blood samples. However, standardization of sampling and access to low-abundance proteins remains problematic. Although, proteomics is playing a major role in the discovery phase of biomarkers, validation in independent populations is necessary by using more specific methods. The knowledge of new HF biomarkers may allow a more personalized medicine in the future.     

A human tissue and data resource: an overview of opportunities,challenges, and development of a provider/researcher partnership model

As we continue to strive to apply the findings of in vitro and animal studies to human disease and transition from genomics to proteomics, we will experience an ever-increasing need for human tissues. A web based system that provides access to tissues repositories and associated data will best facilitate the access to these vital resources and the application of research information to human disease treatment. There are organizational and design requirements that must be addressed in the implementation of the infrastructures that are needed to implement such a system, with special attention paid to the protection of patient anonymity. This report describes the implementation of a prototype human tissue network in the hope of encouraging implementation of similar systems among other consortia of providers and researchers.     

Human kidney glomerulus proteome and biomarker discovery of kidney diseases

The kidney glomerulus is the site of plasma filtration and production of primary urine in the kidney. The structure not only plays a pivotal role in ultrafiltration of plasma into urine but also is the locus of kidney diseases progressing to chronic renal failure. Patients afflicted with these glomerular diseases frequently progress to irreversible loss of renal function and inevitably require replacement therapies. The diagnosis and treatment of glomerular diseases are now based on clinical manifestations, urinary protein excretion level, and renal pathology of needle biopsy specimens. The molecular mechanisms underlying the progression of glomerular diseases are still obscure despite a great number of clinical and experimental studies. Proteomics is a particularly promising approach for the discovery of proteins relevant to physiological and pathophysiological processes, and has been recently employed in nephrology. Although until now most efforts of proteomic analysis have been conducted with urine, the biological fluid that is easily collected without invasive procedures, proteomic analysis of the glomerulus, the tissue most proximal to the disease loci, is the most straightforward approach. In this review, we attempt to outline the current status of clinical proteomics of the glomerulus and provide a perspective of protein biomarker discovery of glomerular diseases.     

2nd Combined Working Group and Management Committee Meeting of Urine and Kidney Proteomics COST Action 29-30 March 2009, Nafplio, Greece

EuroKUP (Urine and Kidney Proteomics; www.eurokup.org) is a COST (European Cooperation in the field of Scientific and Technical research: www.cost.esf.org Action fostering a multi-disciplinary network of investigators from 25 countries and focusing on facilitating translational proteomic research in kidney diseases. Four Working Groups focusing respectively on defining clinically important research questions in kidney diseases, kidney tissue proteomics, urine proteomics and bioinformatics have been generated. The EuroKUP members had their second combined Working Group and Management Committee (MC) meeting in Nafplio, Greece from March 29 to 30, 2009. This report summarizes the main presentations, discussions and agreed action points during this meeting. These refer to the design of collaborative projects and clinical center networks for specific kidney diseases; establishment of guidelines for kidney tissue proteomics analysis by laser-based imaging- and laser capture microdissection-MS; development and characterization of a "standard" urine specimen to be used for assessment of platform capability and data comparability in clinical proteomics applications; definition of statistical requirements in biomarker discovery studies; and development of a specialized kidney and urine ontology. Various training activities are planned involving training schools on laser capture microdissection- and imaging-MS, workshops on ontologies as well as short-term travel grants for junior investigators.     

Clinical Proteomics for Post‐Hematopoeitic Stem Cell Transplantation Outcomes

Allogeneic hematopoietic stem cell transplantation (HSCT) is the most effective form of tumor immunotherapy available to date. However, while HSCT can induce beneficial graft‐versus‐leukemia (GVL) effect, the adverse effect of graft‐versus‐host disease (GVHD), which is closely linked to GVL, is the major source of morbidity and mortality following HSCT. Until recently, available diagnostic and staging tools frequently fail to identify those at higher risk of disease progression or death. Furthermore, there are shortcomings in the prediction of the need for therapeutic interventions or the response rates to different forms of therapy. The past decade has been characterized by an explosive evolution of proteomics technologies, largely due to important advances in high‐throughput MS instruments and bioinformatics. Building on these opportunities, blood biomarkers have been identified and validated both as promising diagnostic tools, prognostic tools that risk‐stratify patients before future occurrence of GVHD and as predictive tools for responsiveness to GVHD therapy and non‐relapse mortality. These biomarkers might facilitate timely and selective therapeutic intervention. This review summarizes current information on clinical proteomics for GVHD as well as other complications following HSCT. Finally, it proposes future directions for the translation of clinical proteomics to discovery of new potential therapeutic targets to the development of drugs.     

基于MVC三层结构的慢性疾病管理的实现

该慢性疾病管理系统由北京大学第三医院肾内科组织开发,目的有:1)开创一种全新的慢性病管理模型:2)为医患搭建一个高效的疾病管理与交流平台;3)鼓励并促进患者的自我管理;4)提供了一个有利于临床科研工作开展的数据仓库.文章在分析了疾病管理系统的现状的基础上,从系统架构、系统功能、系统设计与实现等方面介绍了一个全新的基于Struts+Hibernate的慢性疾病管理系统.