Development of a Fit-For-Purpose Multi-Marker Panel for Early Diagnosis of Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) suffers from a lack of an effective diagnostic method, which hampers improvement in patient survival. Carbohydrate antigen 19-9 (CA19-9) is the only FDA-approved blood biomarker for PDAC, yet its clinical utility is limited due to suboptimal performance. Liquid chromatography-mass spectrometry (LC-MS) has emerged as a burgeoning technology in clinical proteomics for the discovery, verification, and validation of novel biomarkers. A plethora of protein biomarker candidates for PDAC have been identified using LC-MS, yet few has successfully transitioned into clinical practice. This translational standstill is owed partly to insufficient considerations of practical needs and perspectives of clinical implementation during biomarker development pipelines, such as demonstrating the analytical robustness of proposed biomarkers which is critical for transitioning from research-grade to clinical-grade assays. Moreover, the throughput and cost-effectiveness of proposed assays ought to be considered concomitantly from the early phases of the biomarker pipelines for enhancing widespread adoption in clinical settings. Here, we developed a fit-for-purpose multi-marker panel for PDAC diagnosis by consolidating analytically robust biomarkers as well as employing a relatively simple LC-MS protocol. In the discovery phase, we comprehensively surveyed putative PDAC biomarkers from both in-house data and prior studies. In the verification phase, we developed a multiple-reaction monitoring (MRM)-MS-based proteomic assay using surrogate peptides that passed stringent analytical validation tests. We adopted a high-throughput protocol including a short gradient (<10 min) and simple sample preparation (no depletion or enrichment steps). Additionally, we developed our assay using serum samples, which are usually the preferred biospecimen in clinical settings. We developed predictive models based on our final panel of 12 protein biomarkers combined with CA19-9, which showed improved diagnostic performance compared to using CA19-9 alone in discriminating PDAC from non-PDAC controls including healthy individuals and patients with benign pancreatic diseases. A large-scale clinical validation is underway to demonstrate the clinical validity of our novel panel.

Omics Derived Biomarkers and Novel Drug Targets for Improved Intervention in Advanced Prostate Cancer

Prostate cancer (PCa) is one of the most frequently diagnosed malignancies, and the fifth leading cause of cancer related mortality in men. For advanced PCa, radical prostatectomy, radiotherapy, and/or long-term androgen deprivation therapy are the recommended treatment options. However, subsequent progression to metastatic disease after initial therapy results in low 5-year survival rates (29%). Omics technologies enable the acquisition of high-resolution large datasets that can provide insights into molecular mechanisms underlying PCa pathology. For the purpose of this article, a systematic literature search was conducted through the Web of Science Database to critically evaluate recent omics-driven studies that were performed towards: (a) Biomarker development and (b) characterization of novel molecular-based therapeutic targets. The results indicate that multiple omics-based biomarkers with prognostic and predictive value have been validated in the context of PCa, with several of those being also available for commercial use. At the same time, omics-driven potential drug targets have been investigated in pre-clinical settings and even in clinical trials, holding the promise for improved clinical management of advanced PCa, as part of personalized medicine pipelines.

Proteomics biomarkers for solid tumors: Current status and future prospects

Cancer is a heterogeneous multifactorial disease, which continues to be one of the main causes of death worldwide. Despite the extensive efforts for establishing accurate diagnostic assays and efficient therapeutic schemes, disease prevalence is on the rise, in part, however, also due to improved early detection. For years, studies were focused on genomics and transcriptomics, aiming at the discovery of new tests with diagnostic or prognostic potential. However, cancer phenotypic characteristics seem most likely to be a direct reflection of changes in protein metabolism and function, which are also the targets of most drugs. Investigations at the protein level are therefore advantageous particularly in the case of in-depth characterization of tumor progression and invasiveness. Innovative high-throughput proteomic technologies are available to accurately evaluate cancer formation and progression and to investigate the functional role of key proteins in cancer. Employing these new highly sensitive proteomic technologies, cancer biomarkers may be detectable that contribute to diagnosis and guide curative treatment when still possible. In this review, the recent advances in proteomic biomarker research in cancer are outlined, with special emphasis placed on the identification of diagnostic and prognostic biomarkers for solid tumors. In view of the increasing number of screening programs and clinical trials investigating new treatment options, we discuss the molecular connections of the biomarkers as well as their potential as clinically useful tools for diagnosis, risk stratification and therapy monitoring of solid tumors.

Urinary proteomic biomarkers in oncology: ready for implementation?

Introduction: Biomarkers are expected to improve the management of cancer patients by enabling early detection and prediction of therapeutic response. Proteins reflect a molecular phenotype, have high potential as biomarkers, and also are key targets for intervention. Given the ease of collection and proximity to certain tumors, the urinary proteome is a rich source of biomarkers and several proteins have been already implemented. Areas covered: We examined the literature on urine proteins and proteome analysis in oncology from reports published during the last 5 years to generate an overview on the status of urine protein and peptide biomarkers, with emphasis on their actual clinical value. Expert commentary: A few studies report on biomarkers that are ready to be implemented in patient management, among others in bladder cancer and cholangiocarcinoma. These reports are based on multi-marker approaches. A high number of biomarkers, though, has been described in studies with low statistical power. In fact, several of them have been consistently reported across different studies. The latter should be the focus of attention and be tested in properly designed confirmatory and ultimately, prospective investigations. It is expected that multi-marker classifiers for a specific context-of-use, will be the preferred path toward clinical implementation.

Promise and Implementation of Proteomic Prostate Cancer Biomarkers

Prostate cancer is one of the most commonly diagnosed malignancy and the fifth leading cause of cancer mortality in men. Despite the broad use of prostate-specific antigen test that resulted in an increase in number of diagnosed cases, disease management needs to be improved. Proteomic biomarkers alone and or in combination with clinical and pathological risk calculators are expected to improve on decreasing the unnecessary biopsies, stratify low risk patients, and predict response to treatment. To this end, significant efforts have been undertaken to identify novel biomarkers that can accurately discriminate between indolent and aggressive cancer forms and indicate those men at high risk for developing prostate cancer that require immediate treatment. In the era of “big data” and “personalized medicine” proteomics-based biomarkers hold great promise to provide clinically applicable tools, as proteins regulate all biological functions, and integrate genomic information with the environmental impact. In this review article, we aim to provide a critical assessment of the current proteomics-based biomarkers for prostate cancer and their actual clinical applicability. For that purpose, a systematic review of the literature published within the last 10 years was performed using the Web of Science Database. We specifically discuss the potential and prospects of use for diagnostic, prognostic and predictive proteomics-based biomarkers, including both body fluid- and tissue-based markers.

Ten Years of Proteomics in Bladder Cancer: Progress and Future Directions

Research efforts targeting the identification of bladder cancer biomarkers have been extensive during the past decade. Investigations have been performed at the genome, transcriptome, proteome, and metabolome levels and outputs have started appearing including the sketching of disease molecular subtypes. Proteins are directly linked to cell phenotype hence they accumulate special interest as both biomarkers and therapeutic targets. Multiple technical challenges exist, of the main, being the protein concentration vast dynamic range and presence of proteins in modified forms. The scope of this review is to summarize the contribution of proteomics research in this quest of bladder cancer biomarkers. To obtain an unbiased and comprehensive overview, the scientific literature was searched for manuscripts describing proteomic studies on urothelial cancer from the last ten years and those including independent verification studies in urine, tissue and blood are briefly presented. General observations include: a) in most cases, suboptimal experimental design including healthy controls in biomarker discovery and frequently biomarker verification, is followed; b) variability in protein findings between studies can be observed, to some extent reflecting complexity of experimental approaches and proteome itself; c) consistently reported biomarkers include mainly plasma proteins and d) compilation of protein markers into diagnostic panels appears the most promising way forward. Two main avenues of research can now be foreseen: targeting integration of the existing disparate data with proteomic findings being placed in the context of existing knowledge on bladder cancer subtypes and in parallel, accumulation of clinical samples to support proper validation studies of promising marker combinations.

Proteomics for prediction of disease progression and response to therapy in diabetic kidney disease

The past decade has resulted in multiple new findings of potential proteomic biomarkers of diabetic kidney disease (DKD). Many of these biomarkers reflect an important role in the (patho)physiology and biological processes of DKD. Situations in which proteomics could be applied in clinical practice include the identification of individuals at risk of progressive kidney disease and those who would respond well to treatment, in order to tailor therapy for those at highest risk. However, while many proteomic biomarkers have been discovered, and even found to be predictive, most lack rigorous external validation in sufficiently powered studies with renal endpoints. Moreover, studies assessing short-term changes in the proteome for therapy-monitoring purposes are lacking. Collaborations between academia and industry and enhanced interactions with regulatory agencies are needed to design new, sufficiently powered studies to implement proteomics in clinical practice.

Advances in urinary proteome analysis and applications in systems biology

The urinary proteome is the focus of many studies due to the ease of urine collection and the relative proteome stability. Systems biology allows the combination of multiple omics studies, forming a link between proteomics, metabolomics, genomics and transcriptomics. In-depth data interpretation is achieved by bioinformatics analysis of -omics data sets. It is expected that the contribution of systems biology to the study of the urinary proteome will offer novel insights. The main focus of this review is on technical aspects of proteomics studies, available tools for systems biology analysis and the application of urinary proteomics in clinical studies and systems biology.

Expression of cyclin D1 and cyclin E in urothelial bladder carcinoma detected in tissue chips using a quantum dot immunofluorescence technique

The present study aimed to investigate the expression of cyclin D1 and cyclin E in tissue chips of bladder cancer using quantum dots (QDs), as well as examine its clinicopathological significance. The QD-based immunofluorescence tissue chemical technique was adopted to detect cyclin D1 and cyclin E expression in 75 tissue chips of human urothelial bladder carcinoma (including 70 cases of urothelial bladder carcinoma and 5 cases of cystitis), and its correlation with clinicopathological features was analyzed. The positive rates of cyclin D1 and cyclin E expression in urothelial bladder carcinoma were 68.6% (48/70) and 70.0% (49/70), respectively; however, no expression was observed in cystitis. Based on the results of statistical analysis, the difference in the positive rates of cyclin D1 and cyclin E expression between urothelial bladder carcinoma and cystitis was significant (P<0.05). QD staining and statistical analysis revealed that the expression of cyclin D1 and cyclin E in urothelial bladder carcinoma was significantly higher compared with that in cystitis (P<0.05). However, no statistically significant difference (P>0.05) in cyclin D1 expression was observed in relation to pathological stage, clinical stage or invasion of urothelial bladder carcinoma; however, there was a significant difference (P<0.05) in cyclin E expression with respect to these factors. These results demonstrated that overexpression of cyclin D1 may be an early event in the occurrence of urothelial bladder carcinoma. Cyclin D1 may play a role in the initial stage where cell proliferation is a necessary step, without invasion or metastasis. In addition, overexpression of cyclin E was correlated with the stage and depth of invasion of urothelial bladder carcinoma. In conclusion, the abnormal expression of cyclin D1 and cyclin E may be involved in the occurrence and development of urothelial bladder carcinoma.

Epidemiologic design and analysis for proteomic studies: a primer on -omic technologies

Proteome analysis is increasingly being used in investigations elucidating the molecular basis of disease, identifying diagnostic and prognostic markers, and ultimately improving patient care. We appraised the current status of proteomic investigations using human samples, including the state of the art in proteomic technologies, from sample preparation to data evaluation approaches, as well as key epidemiologic, statistical, and translational issues. We systematically reviewed the most highly cited clinical proteomic studies published between January 2009 and March 2014 that included a minimum of 100 samples, as well as strategies that have been successfully implemented to enhance the translational relevance of proteomic investigations. Limited comparability between studies and lack of specification of biomarker context of use are frequently observed. Nevertheless, there are initial examples of successful biomarker discovery in cross-sectional studies followed by validation in high-risk longitudinal cohorts. Translational potential is currently hindered, as limitations in proteomic investigations are not accounted for. Interdisciplinary communication between proteomics experts, basic researchers, epidemiologists, and clinicians, an orchestrated assimilation of required resources, and a more systematic translational outlook for accumulation of evidence may augment the public health impact of proteomic investigations.

IMAC fractionation in combination with LC-MS reveals H2B and NIF-1 peptides as potential bladder cancer biomarkers

Improvement in bladder cancer (BC) management requires more effective diagnosis and prognosis of disease recurrence and progression. Urinary biomarkers attract special interest because of the noninvasive means of urine collection. Proteomic analysis of urine entails the adoption of a fractionation methodology to reduce sample complexity. In this study, we applied immobilized metal affinity chromatography in combination with high-resolution LC-MS/MS for the discovery of native urinary peptides potentially associated with BC aggressiveness. This approach was employed toward urine samples from patients with invasive BC, noninvasive BC, and benign urogenital diseases. A total of 1845 peptides were identified, corresponding to a total of 638 precursor proteins. Specific enrichment for proteins involved in nucleosome assembly and for zinc-finger transcription factors was observed. The differential expression of two candidate biomarkers, histone H2B and NIF-1 (zinc finger 335) in BC, was verified in independent sets of urine samples by ELISA and by immunohistochemical analysis of BC tissue. The results collectively support changes in the expression of both of these proteins with tumor progression, suggesting their potential role as markers for discriminating BC stages. In addition, the data indicate a possible involvement of NIF-1 in BC progression, likely as a suppressor and through interactions with Sox9 and HoxA1.

Network views for personalized medicine

Clinical Proteomics has traveled a long way pinpointing potential biomarkers for a variety of diseases. However, the absence of clinical implementation of proteomics findings has led to a frank evaluation and reconsideration of applied practices in biomarker discovery, recruitment of technological tools for biomarker verification and generation of new guidelines for data reporting. Nevertheless, considering the need for vast clinical resources for biomarker validation, the frequent lack of clear definitions of contexts of use, in combination to the biomarker "high offer," progress toward biomarker implementation will even more require the adoption of an extensive open-minded approach: disease-focused networks are needed to ensure rapid exchange of information, initiation of appropriate studies, parallel validation of multiple biomarkers and sharing of valuable clinical resources. This viewpoint article targets to reflect on these issues and advocates the added value of multidisciplinary networks in biomarker development using bladder cancer as a paradigm.

How to get proteomics to the clinic? Issues in clinical proteomics, exemplified by CE-MS

Clinical proteomics is defined as application of proteome analysis aiming at improving the current clinical situation. As such, the success of clinical proteomics should be assessed based on the clinical impact following implementation of the findings. While we have experienced significant technological advancements in mass spectrometry in the last years, based on the above measure, this has not at all resulted in similar advancements in clinical proteomics. Although a large number of proteomic biomarkers have been described, most of them were not subsequently validated, and certainly have had no impact in clinical decision making as yet. Under the current conditions, it appears likely that the situation will not change significantly: we will be flooded by reports on biomarkers, but not see any implementation. In this article, some key issues in proteomic biomarker research are pinpointed, based on the experience with CE-MS, likely also holding true for biomarkers resulting from other analysis domains.