Proteomics in human cancer research

Proteomics is now widely employed in the study of cancer. Many laboratories are applying the rapidly emerging technologies to elucidate the underlying mechanisms associated with cancer development, progression, and severity in addition to developing drugs and identifying patients who will benefit most from molecular targeted compounds. Various proteomic approaches are now available for protein separation and identification, and for characterization of the function and structure of candidate proteins. In spite of significant challenges that still exist, proteomics has rapidly expanded to include the discovery of novel biomarkers for early detection, diagnosis and prognostication (clinical application), and for the identification of novel drug targets (pharmaceutical application). To achieve these goals, several innovative technologies including 2-D-difference gel electrophoresis, SELDI, multidimensional protein identification technology, isotope-coded affinity tag, solid-state and suspension protein array technologies, X-ray crystallography, NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulation have evolved, and are being used in different combinations. This review provides an overview of the field of proteomics and discusses the key proteomic technologies available to researchers. It also describes some of the important challenges and highlights the current pharmaceutical and clinical applications of proteomics in human cancer research.     

Proteins that underlie neoplastic progression of ulcerative colitis

Patients with ulcerative colitis (UC) have an increased risk for developing colorectal cancer. Because UC tumorigenesis is associated with genomic field defects that can extend throughout the entire colon, including the non‐dysplastic mucosa, we hypothesized that the same field defects will include abnormally expressed proteins. Here, we applied proteomics to study the protein expression of UC neoplastic progression. The protein profiles of colonic epithelium were compared with (i) UC patients without dysplasia (non‐progressors), (ii) non‐dysplastic colonic tissue from UC patient with high‐grade dysplasia or cancer (progressors), (iii) high‐grade dysplastic tissue from UC progressors, and (iv) normal colon. We identified differential protein expression associated with UC neoplastic progression. Proteins relating to mitochondria, oxidative activity, and calcium‐binding proteins were some of the interesting classes of these proteins. Network analysis discovered that Sp1 and c‐myc proteins may play roles in UC early and late stages of neoplastic progression, respectively. Two over‐expressed proteins in the non‐dysplastic tissue of UC progressors, carbamoyl‐phosphate synthase 1 and S100P, were further confirmed by immunohistochemistry analysis. Our study provides insight into the molecular events associated with UC neoplastic progression, which could be exploited for the development of protein biomarkers in fields of non‐dysplastic mucosa that identify a patient's risk for UC dysplasia.     

Coupling enrichment methods with proteomics for understanding and treating disease

Owing to recent advances in proteomics analytical methods and bioinformatics capabilities there is a growing trend toward using these capabilities for the development of drugs to treat human disease, including target and drug evaluation, understanding mechanisms of drug action, and biomarker discovery. Currently, the genetic sequences of many major organisms are available, which have helped greatly in characterizing proteomes in model animal systems and humans. Through proteomics, global profiles of different disease states can be characterized (e.g. changes in types and relative levels as well as changes in PTMs such as glycosylation or phosphorylation). Although intracellular proteomics can provide a broad overview of physiology of cells and tissues, it has been difficult to quantify the low abundance proteins which can be important for understanding the diseased states and treatment progression. For this reason, there is increasing interest in coupling comparative proteomics methods with subcellular fractionation and enrichment techniques for membranes, nucleus, phosphoproteome, glycoproteome as well as low abundance serum proteins. In this review, we will provide examples of where the utilization of different proteomics-coupled enrichment techniques has aided target and biomarker discovery, understanding the drug targeting mechanism, and mAb discovery. Taken together, these improvements will help to provide a better understanding of the pathophysiology of various diseases including cancer, autoimmunity, inflammation, cardiovascular disease, and neurological conditions, and in the design and development of better medicines for treating these afflictions.     

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.     

Proteomic identification of proteins in the human brain: Towards a more comprehensive understanding of neurodegenerative disease

Proteomics has revealed itself as a powerful tool in the identification and determination of proteins and their biological significance. More recently, several groups have taken advantage of the high-throughput nature of proteomics in order to gain a more in-depth understanding of the human brain. In turn, this information has provided researchers with invaluable insight into the potential pathways and mechanisms involved in the pathogenesis of several neurodegenerative disorders, e.g., Alzheimer and Parkinson disease. Furthermore, these findings likely will improve methods to diagnose disease and monitor disease progression as well as generate novel targets for therapeutic intervention. Despite these advances, comprehensive understanding of the human brain proteome remains challenging, and requires development of improved sample enrichment, better instrumentation, and innovative analytic techniques. In this review, we will focus on the most recent progress related to identification of proteins in the human brain under normal as well as pathological conditions, mainly Alzheimer and Parkinson disease, their potential application in biomarker discovery, and discuss current advances in protein identification aimed at providing a more comprehensive understanding of the brain.     

Potential biomarkers for oral squamous cell carcinoma: Proteomics discovery and clinical validation

Oral squamous cell carcinoma (OSCC) is the worldwide concerned cancer. In spite of the advances in treatment, the 5-year survival rate has only increased subtly during the past two decades, which is largely due to the advanced stages of disease at diagnosis and the frequent development of relapse and second primary tumors. Therefore, the identification of underlying OSCC protein biomarker during cancer initiation and progression could aid the diagnosis and treatment of OSCC. In this review, recent researches on proteomics analysis of tissue, saliva, and serum for early detection and evaluation aggressiveness and occurrence of OSCC were summarized. The emphasis is placed on early detection by tissues, saliva, and serum of patients with histologically defined OSCC patients. Although lots of researches for searching OSCC protein biomarker have done, few common protein biomarkers have been detected. Low-redundant protein in tissues, saliva, and serum from OSCC may more accurately reflected the progression of OSCC, so novel approach for the depth research strategy and the sample choice for proteomics are of importance in OSCC biomarker discovery.     

Proteomics of Alzheimer's disease: Unveiling protein dysregulation in complex neuronal systems

Alzheimer's disease (AD) and its progressive dementia is multifactorial, develops relatively sporadically, and involves multiple pathologies in the complex biological system of the brain. For these reasons, genetics alone is not likely to explain the molecular basis of this disease. Proteomics is contributing valuable information about the underlying molecular defects involved in AD development and progression, which includes oxidative damage to specific proteins, altered levels of synaptic components, and protein compositions of Aβ plaques and neurofibrillary tangles (pathological hallmarks of AD). However, emerging strategies in the field of proteomics which include more specific targeting of disease-related anatomical regions, targeting of specific subcellular compartments of functional relevance, novel approaches for large scale identification of regulatory post-translational modifications such as phosphorylation and O-GlcNAc, improved chromatographic separations of peptides for more comprehensive analysis of samples, and high-throughput quantitative strategies directly coupled with MS should greatly enhance the future of AD proteomics. The characterization of AD-specific alterations in proteomes should provide further insight into mechanisms of disease development and progression, provide biomarkers predicting disease development, and provide novel targets for therapeutic intervention.     

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.     

Proteomics and genomics of urinary bladder cancer

Urinary bladder cancer is the fifth most common cancer in the United States. The National Cancer Institute estimates that the incidence rates will be 68 810 and the mortality rate will be 14 100 in the year 2008. Although the gold standards cytology and cystoscopy are specific for diagnosing bladder cancer, the former lacks the sensitivity to detect low‐grade tumors and the latter is very invasive and expensive. Therefore, scientists are interested in identifying reliable non‐invasive biomarkers that could be utilized in screening, leading to early detection and/or in predicting the progression of superficial tumors to invasive higher‐stage lesions with high specificity and sensitivity. Several biomarkers that indicate changes in the expression of proteins associated with increased risk have been identified. The purpose of this analysis is to provide an overview of the studies that have been conducted during the last decade that identify diagnostic and prognostic biomarkers via proteomic and genomic advancements.     

CD317 在肿瘤发生发展及治疗方面的研究进展

CD317(Tetherin、BST-2 或 HM1.24)是由 BST-2 基因编码的一个结构独特的 II 型跨膜糖蛋白, 在多种人体组织中组成型表达,也可被干扰素等细胞因子诱导。近年来,越来越多的研究表明,CD317 在多种肿瘤中表达上调,广泛参与肿瘤细胞增殖、迁移以及凋亡抵抗等生物学过程从而促进肿瘤的发 生发展,是肿瘤治疗的潜在靶点。该文聚焦肿瘤领域,总结 CD317 的表达模式、作用机制以及靶向策 略的相关进展,为肿瘤发病理论研究、治疗策略开发提供新的思考和方向。     

Proteomics in diabetic nephropathy

Diabetes mellitus (DM) is currently one of the principal causes of end stage renal disease (ESRD). Approximately 40% of all diabetic patients eventually develop diabetic nephropathy (DN). The complexity of diabetes and its complications require a broad-based, unbiased, scientific approach, such as proteomics, in order to understand the progression of DN. Proteomic techniques have been applied extensively to explore the complexity of the mechanisms associated with DN, and to identify novel biomarkers and therapeutic targets. This review provides insights into how proteomics can be applied to DN, and how experimental data can be linked to clinical applications. In addition, recent proteome studies of DN are summarized. The rapid rate of development of the relevant technologies, along with the combination of classic physiological and biochemical techniques with proteomics will facilitate new discoveries.     

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.     

Mass spectrometry in clinical proteomics - from the present to the future

MS is an important analytical tool in clinical proteomics, primarily in the disease-specific discovery, identification and characterisation of proteomic biomarkers and patterns. MS-based proteomics is increasingly used in clinical validation and diagnostic method development. The latter departs from the typical application of MS-based proteomics by exchanging some of the high performance of analysis for the throughput, robustness and simplicity required for clinical diagnostics. Although conventional MS-based proteomics has become an important field in clinical applications, some of the most recent MS technologies have not yet been extensively applied in clinical proteomics. In this review, we will describe the current state of MS in clinical proteomics and look to the future of this field.     

New horizon for breast cancer biomarker discoveries: What might the liquid biopsy of nipple aspirate fluid hold?

The existence of cellular, molecular and biochemical heterogeneity of human breast cancers reveals the intricacy of biomarkers complexity, stimulating studies on new approaches (like “liquid biopsies”) for the improvements in precision medicine. Breast cancer is recognized as a leading cause of morbidity and mortality worldwide with tumors significantly diverse and containing many types of cells showing different genetic and epigenetic profiles. In this field, the technology of liquid biopsy (applied to a fluid produced by breast gland, named nipple aspirate fluids, NAF) highlights the power of combining basic and clinical research. NAF is the mirror of the entire ductal/alveolar breast tree providing almost complete proteomic profile and a valuable source for biomarker discovery, in non‐invasive manner than tissue biopsies. The liquid biopsy technology using NAF may represent the outstanding breakthrough of proteomic cancer research revealing novel diagnostic and prognostic applications. In conjunction to metabolomic and degradome profiling, the use of NAF as liquid biopsy approach will improve the detection of changes in the cellular microenvironment of the breast tumors, understanding molecular and biochemical mechanisms which drive breast tumor initiation, maintenance and progression, and finally enhancing the development of novel drug targets and new treatment strategies.     

Application of quantitative proteomics technologies to the biomarker discovery pipeline for multiple sclerosis

Multiple sclerosis is an inflammatory-mediated demyelinating disorder most prevalent in young Caucasian adults. The various clinical manifestations of the disease present several challenges in the clinic in terms of diagnosis, monitoring disease progression and response to treatment. Advances in MS-based proteomic technologies have revolutionized the field of biomarker research and paved the way for the identification and validation of disease-specific markers. This review focuses on the novel candidates discovered by the application of quantitative proteomics to relevant disease-affected tissues in both the human context and within the animal model of the disease known as experimental autoimmune encephalomyelitis. The role of targeted MS approaches for biomarker validation studies, such as multiple reaction monitoring will also be discussed.     

Differential expression of serum/plasma proteins in various infectious diseases: Specific or nonspecific signatures

Apart from direct detection of the infecting organisms or biomarker of the pathogen itself, surrogate host markers are also useful for sensitive and early diagnosis of pathogenic infections. Early detection of pathogenic infections, discrimination among closely related diseases with overlapping clinical manifestations, and monitoring of disease progression can be achieved by analyzing blood biomarkers. Therefore, over the last decade large numbers of proteomics studies have been conducted to identify differentially expressed human serum/plasma proteins in different infectious diseases with the intent of discovering novel potential diagnostic/prognostic biomarkers. However, in-depth review of the literature indicates that many reported biomarkers are altered in the same way in multiple infectious diseases, regardless of the type of infection. This might be a consequence of generic acute phase reactions, while the uniquely modulated candidates in different pathogenic infections could be indicators of some specific responses. In this review article, we will provide a comprehensive analysis of differentially expressed serum/plasma proteins in various infectious diseases and categorize the protein markers associated with generic or specific responses. The challenges associated with the discovery, validation, and translational phases of serum/plasma biomarker establishment are also discussed.     

Membrane Proteome of Invasive Retinoblastoma: Differential Proteins and Biomarkers

Purpose: Retinoblastoma (RB) is a pediatric ocular cancer which is caused due to the aberrations in the RB1 gene. The changes in the membrane proteomics would help in understanding the development of the retinoblastoma and could identify candidates for biomarkers and therapy. Experimental design: Quantitative proteomics is performed on the enriched membrane fractions from pooled normal retina (n = 5) and pooled retinoblastoma tissues (n = 5). The proteins are tryptic‐digested and tagged with iTRAQ labels. Orbitrap mass spectrometry is used to analyze and quantify the deregulated membrane proteins involved in the RB tumor progression. Immunohistochemistry (IHC) is used to further validate few of the differentially expressed proteins. Results: A total of 3122 proteins are identified of which, 663 proteins are found to be deregulated with ≥two fold change in the RB tumor compared to the retina. 282 proteins are upregulated and 381 are downregulated with ≥2 peptide identifications. Bioinformatic analysis revealed that, most of the proteins are involved in the transport, cellular communication, and growth. Overexpression of lamin B1 (LMNB1) and transferrin receptor (TFRC) are observed in RB tumors using IHC. Conclusion and clinical relevance: The present study, is the first comprehensive quantitative membrane proteomic atlas of the differentially regulated proteins in RB compared to the retina. LMNB1 and TFRC could be potential biomarkers for this childhood cancer.