Proteomics and translational medicine: molecular biomarkers for cancer diagnosis, prognosis and prediction of therapy outcome

Proteomic Analysis of Radiation-Induced Acute Liver Damage in a Rabbit Model

Radiation-induced liver damage (RILD) has become a limitation in radiotherapy for hepatocellular carcinoma. We established a rabbit model of RILD by CyberKnife. Electron microscopy analysis revealed obvious nuclear atrophy and disposition of fat in the nucleus after irradiation. We then utilized a mass spectrometry-based label-free relative quantitative proteomics approach to compare global proteomic changes of rabbit liver in response to radiation. In total, 2365 proteins were identified, including 338 proteins that were significantly dysregulated between irradiated and nonirradiated liver tissues. These differentially expressed proteins included USP47, POLR2A, CSTB, MCFD2, and CSNK2A1. Real-time polymerase chain reaction confirmed that USP47 and CABLES1 transcripts were significantly higher in irradiated liver tissues, whereas MCFD2 and CSNK2A1 expressions were significantly reduced. In Clusters of Orthologous Groups of proteins analysis, differentially expressed proteins were annotated and divided into 24 categories, including posttranslational modification, protein turnover, and chaperones. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the enriched pathways in dysregulated proteins included the vascular endothelial growth factors (VEGF) signaling pathway, the mitogen-activated protein kinase (MAPK) signaling pathway, and the adipocytokine signaling pathway. The identification of proteins and pathways is crucial toward elucidating the radiation response process of the liver, which may facilitate the discovery of novel therapeutic targets.

Identification of peptide regions of SERPINA1 and ENOSF1 and their protein expression as potential serum biomarkers for gastric cancer

This study aimed to detect potential serum biomarkers for gastric cancer. In the present study, we used magnetic bead-based purification and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to detect potential serum markers in 70 gastric cancer (GC) patients compared with 72 healthy controls. On average, up to 81 peaks, of which 11 were significantly different m/z peaks (fold change >1.5; P < 0.001, Wilcoxon rank sum test) between GC group and healthy controls were detected. Two potential gastric serum biomarkers (m/z values of 1546.02 and 5335.08), with higher and specific expression in GC patients were further identified as peptide regions of SERPINA1 and ENOSF1. Enzyme-linked immunosorbent assays (ELISAs) were used to analyze 210 additional serum samples obtained from 36 healthy volunteers, 36 GC patients, 30 GU patients, 36 nonsmall-cell lung cancer (NSCLC) patients, 36 clear-cell renal cell carcinoma (CCRCC) patients, and 36 pancreatic cancer patients to verify the expression of SERPINA1 and ENOSF1 in GC sera. The suitability of the present method for gastric serum proteomic analysis was demonstrated and led to the identification of two peptide regions and their corresponding proteins as potential serum biomarkers for the serum detection of GC.

Identification of potential serum proteomic biomarkers for clear cell renal cell carcinoma

Objective

To investigate discriminating protein patterns and serum biomarkers between clear cell renal cell carcinoma (ccRCC) patients and healthy controls, as well as between paired pre- and post-operative ccRCC patients.

Methods

We used magnetic bead-based separation followed by matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) to identify patients with ccRCC. A total of 162 serum samples were analyzed in this study, among which there were 58 serum samples from ccRCC patients, 40 from additional paired pre- and post-operative ccRCC patients (n = 20), and 64 from healthy volunteers as healthy controls. ClinProTools software identified several distinct markers between ccRCC patients and healthy controls, as well as between pre- and post-operative patients.

Results

Patients with ccRCC could be identified with a mean sensitivity of 88.38% and a mean specificity of 91.67%. Of 67 m/z peaks that differed among the ccRCC, healthy controls, pre- and post-operative ccRCC patients, 24 were significantly different (P<0.05). Three candidate peaks, which were upregulated in ccRCC group and showed a tendency to return to healthy control values after surgery, were identified as peptide regions of RNA-binding protein 6 (RBP6), tubulin beta chain (TUBB), and zinc finger protein 3 (ZFP3) with the m/z values of 1466.98, 1618.22, and 5905.23, respectively.

Conclusion

MB-MALDI-TOF-MS method could generate serum peptidome profiles of ccRCC, and provide a new approach to identify potential biomarkers for diagnosis as well as prognosis of this malignancy.

Quantitative evaluation of translational medicine based on scientometric analysis and information extraction

Designed to advance the two-way translational process between basic research and clinical practice, translational medicine has become one of the most important areas in biomedicine. The quantitative evaluation of translational medicine is valuable for the decision making of global translational medical research and funding. Using the scientometric analysis and information extraction techniques, this study quantitatively analyzed the scientific articles on translational medicine. The results showed that translational medicine had significant scientific output and impact, specific core field and institute, and outstanding academic status and benefit. While it is not considered in this study, the patent data are another important indicators that should be integrated in the relevant research in the future.

Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development

Biomarker research is continuously expanding in the field of clinical proteomics. A combination of different proteomic-based methodologies can be applied depending on the specific clinical context of use. Moreover, current advancements in proteomic analytical platforms are leading to an expansion of biomarker candidates that can be identified. Specifically, mass spectrometric techniques could provide highly valuable tools for biomarker research. Ideally, these advances could provide with biomarkers that are clinically applicable for disease diagnosis and/ or prognosis. Unfortunately, in general the biomarker candidates fail to be implemented in clinical decision making. To improve on this current situation, a well-defined study design has to be established driven by a clear clinical need, while several checkpoints between the different phases of discovery, verification and validation have to be passed in order to increase the probability of establishing valid biomarkers. In this review, we summarize the technical proteomic platforms that are available along the different stages in the biomarker discovery pipeline, exemplified by clinical applications in the field of bladder cancer biomarker research.

Protein biomarkers distinguish between high- and low-risk pediatric acute lymphoblastic leukemia in a tissue specific manner

The current study evaluated the differential expression detected in the proteomic profiles of low risk- and high risk- ALL pediatric patients to characterize candidate biomarkers related to diagnosis, prognosis and patient targeted therapy. Bone marrow and peripheral blood plasma and cell lysates samples were obtained from pediatric patients with low- (LR) and high-risk (HR) ALL at diagnosis. As controls, non-leukemic pediatric patients were studied. Cytogenetic analysis was carried out by G- banding and interphase fluorescent in situ hybridization. Differential proteomic analysis was performed using two-dimensional gel electrophoresis and protein identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The differential expression of certain proteins was confirmed by Western blot analysis. The obtained data revealed that CLUS, CERU, APOE, APOA4, APOA1, GELS, S10A9, AMBP, ACTB, CATA and AFAM proteins play a significant role in leukemia prognosis, potentially serving as distinctive biomarkers for leukemia aggressiveness, or as suppressor proteins in HR-ALL cases. In addition, vitronectin and plasminogen probably contributed to leukemogenesis, whilst bicaudal D-related protein 1 could afford a significant biomarker for pediatric ALL therapeutics.

Phosphoproteomics and lung cancer research

Massive evidence suggests that genetic abnormalities contribute to the development of lung cancer. These molecular abnormalities may serve as diagnostic, prognostic and predictive biomarkers for this deadly disease. It is imperative to search these biomarkers in different tumorigenesis pathways so as to provide the most appropriate therapy for each individual patient with lung malignancy. Phosphoproteomics is a promising technology for the identification of biomarkers and novel therapeutic targets for cancer. Thousands of proteins interact via physical and chemical association. Moreover, some proteins can covalently modify other proteins post-translationally. These post-translational modifications ultimately give rise to the emergent functions of cells in sequence, space and time. Phosphoproteomics clinical researches imply the comprehensive analysis of the proteins that are expressed in cells or tissues and can be employed at different stages. In addition, understanding the functions of phosphorylated proteins requires the study of proteomes as linked systems rather than collections of individual protein molecules. In fact, proteomics approaches coupled with affinity chromatography strategies followed by mass spectrometry have been used to elucidate relevant biological questions. This article will discuss the relevant clues of post-translational modifications, phosphorylated proteins, and useful proteomics approaches to identify molecular cancer signatures. The recent progress in phosphoproteomics research in lung cancer will be also discussed.

The international effort: building the bridge for Translational Medicine: Report of the 1st International Conference of Translational Medicine (ICTM)

BACKGROUND

Supported by the International Society for Translational Medicine (ISTM), Wenzhou Medical College and the First Affiliated Hospital of Wenzhou Medical College, the International Conference on Translational Medicine (ICTM) was held on October 22-23, 2011 in Wenzhou, China. Nearly 800 registrants attended the meeting, primarily representing institutes and hospitals in Europe, The United States of America, And Asia, and China. The meeting was chaired and organized by Dr. Xiangdong Wang, Xiaoming Chen, Richard Coico, Jeffrey M. Drazen, Richard Horton, Francesco M. Marincola, Laurentiu M. Popescu, Jia Qu and Aamir Shahzad.

FINDINGS

The meeting focused on the communication of the need to foster translational medicine (TM) by building and broadening bridges between basic research and clinical studies at the international level. The meeting included distinguished TM experts from academia, the pharmaceutical and diagnostics industries, government agencies, regulators, and clinicians and provided the opportunity to identify shared interests and efforts for collaborative approaches utilizing cutting edge technologies, innovative approaches and novel therapeutic interventions. The meeting defined the concept of TM in its two-way operational scheme and emphasized the need for bed to bench efforts based directly on clinical observation.

CONCLUSIONS

It was the meeting participants' realization that the shared main goals of TM include breaking the separation between clinic practice and basic research, establishing positive feedback by understanding the basis of expected and unexpected clinical outcomes and accelerating basic research relevant to human suffering. The primary objectives of the meeting were two-fold: to accelerate the two-way translation by informing the participants representing the different disciplines about the state of art activities around TM approaches; and to identify areas that need to be supported by redirecting limited resources as well as identifying new sources of funding. This report summarizes key concepts presented during the meeting representing the state-of-art translational research and salient aspects of the ensuing discussions.

Mass spectrometry-based protein assays for in vitro diagnostic testing

Mass spectrometry-based protein assays hold great promise for in vitro diagnostic testing. Technological advances in mass spectrometry have given rise to instruments and methods that are fully capable of automated and high-throughput protein assaying. Yet, the numerous steps involved in such assays can lead to difficulties in assay characterization and validation, and can also make them unnecessarily complex and prohibitively expensive for everyday use. Simplification of both approaches and instrumentation seems to be the solution to the fast introduction of the mass spectrometry-based assays into the clinical laboratories. One such simplified approach is the mass spectrometric immunoassay, which couples targeted immunoaffinity protein separation with the power of mass spectrometry detection. Several mass spectrometric immunoassays have been extensively characterized and have found their way into clinical laboratory improvement amendments-certified laboratories in the form of laboratory developed tests. Reviewed in this special report is the development and validation of one of those assays - a Cystatin mass spectrometric immunoassay. With the added advantage of protein variant detection and quantification, these assays can redefine our view of protein diversity, with clear implications in biomarker discovery, validation, and ultimately, in vitro diagnostic testing.

[Proteome profiling for the identification of lung cancer signatures]

在新近蛋白质组学的发展中，对疾病蛋白质组的综合和深入研究已成为重要议题。已有研究报道了在包括肺癌在内的不同疾病中发现的一些生物标志物，有一些在肺癌诊断和预测中有潜在价值。然而，它们很少作为器官特异性生物标志物以充分比较不同肿瘤类别的模型。本文评价了最近发表的一项在不同基因工程小鼠模型中进行比较蛋白质组的研究，并阐明已发现标志物在人肺癌诊断中的有效性及应用。

Proteome profiling for the identification of lung cancer signatures

Comprehensive and in-depth discovery of the disease proteome is an important issue in recent proteomics developments. Previous studies have shown a number of biomarkers discovered in various diseases, including lung cancer. Some of them are potentially useful in lung cancer diagnostics and prognostics. However, few of them can act as organ-specific biomarkers to extensively compare multiple cancer models. This article evaluates a recently published study employing comparative proteomics on multiple genetically engineered mouse models and sheds light on the usefulness and application of the discovered marker panel for human lung cancer diagnostics.

Translational researches require effective protocols for knowledge and technology transfer and integration

Integration of several disciplines (nonclinical, preclinical and clinical researches) during drug discovery and development through learning and confirmation process needs a dynamic process; "translational medicine" (TM) to give a holistic understanding of the entire process. To achieve the highest impacts, however, effective standard protocols need to be performed.