Tissue culture-based breast cancer biomarker discovery platform

Current cancer biomarkers suffer from low diagnostic sensitivity and specificity and have not yet made a major impact on reducing cancer burden. Proteomic methods based on mass spectrometry have matured significantly over the past few years and hold promise to deliver candidate markers for diagnosis, prognosis or monitoring therapeutic response. Because of the complex nature of biological fluids such as plasma, biomarker discovery efforts using proteomics have not as yet delivered any novel tumor markers. Recently, there has been a rise in the number of publications utilizing a cell culture-based model of cancer to identify novel candidate tumor markers. The secretome of cancer cell lines constitutes an important class of proteins that can act locally and systemically in the body. Secreted proteins, in addition to serving as serological markers, play a central role in physiology and pathophysiology. In this review, we focus on the proteomics of breast cancer and the different strategies to mine for biomarkers, with particular emphasis on a cell culture-based model developed in our laboratory.     

5-fluorouracil: mechanisms of action and clinical strategies

5-fluorouracil (5-FU) is widely used in the treatment of cancer. Over the past 20 years, increased understanding of the mechanism of action of 5-FU has led to the development of strategies that increase its anticancer activity. Despite these advances, drug resistance remains a significant limitation to the clinical use of 5-FU. Emerging technologies, such as DNA microarray profiling, have the potential to identify novel genes that are involved in mediating resistance to 5-FU. Such target genes might prove to be therapeutically valuable as new targets for chemotherapy, or as predictive biomarkers of response to 5-FU-based chemotherapy.     

Methodological and practical challenges for personalized cancer therapies

Many experts agree that personalized cancer medicine, defined here as treatment based on the molecular characteristics of a tumor from an individual patient, has great potential in the therapy of many types of cancer. Although targeted therapy agents are increasingly available for clinical applications, many of these promising drugs have produced disappointing results when tested in clinical trials, indicating that there are many challenges that must be addressed to advance this field. We propose that a new generation of clinical trials requiring biopsies to obtain relevant tumor specimens, as well as novel statistical designs, will be essential to improve treatment outcomes. However, these novel clinical trials will only be successful if appropriate biomarkers are identified to help guide the selection of the most beneficial treatments for the participating patients. Although biomarkers based on single gene mutations are the most commonly used in clinical applications today, gene-expression or protein-expression 'signatures' and new imaging technologies have the potential to play important roles as biomarkers in the future. Therefore, it is of crucial importance that we identify and resolve existing challenges that may impede the rapid identification and translation of validated biomarkers with acceptable sensitivity and specificity from the laboratory to the clinic. These challenges include limitations of current biomarker development methodologies and regulatory and reimbursement policies and practices.     

Breast cancer revisited using DNA array-based gene expression profiling

Breast cancer is a complex genetic disease characterized by the accumulation of multiple molecular alterations. The resulting clinical heterogeneity makes current diagnostic and therapeutic strategies less than perfectly adapted to each patient. Pathological and clinical factors are insufficient to capture the complex cascade of events that drive the clinical behavior of tumors. High-throughput molecular technologies provide novel tools to tackle this complexity. In particular, DNA arrays allow the simultaneous and quantitative analysis of the mRNA expression levels of thousands of genes in a single assay. Potential applications are multiple in the cancer field and the first research results are promising; comprehensive gene expression profiles of breast tumors are providing insights into mammary oncogenesis and are revealing new tumor subgroups previously indistinguishable. Significant advances will be the identification of new diagnostic, prognostic and predictive biomarkers as well as the discovery of new potential therapeutic targets. This review presents recent applications of DNA arrays in breast cancer research and discusses some issues to address in the near future to allow the technology to reach its full potential.     

Precision medicine for gastrointestinal cancer: Recent progress and future perspective

Gastrointestinal (GI) cancer has a high tumor incidence and mortality rate worldwide. Despite significant improvements in radiotherapy, chemotherapy, and targeted therapy for GI cancer over the last decade, GI cancer is characterized by high recurrence rates and a dismal prognosis. There is an urgent need for new diagnostic and therapeutic approaches. Recent technological advances and the accumulation of clinical data are moving toward the use of precision medicine in GI cancer. Here we review the application and status of precision medicine in GI cancer. Analyses of liquid biopsy specimens provide comprehensive real-time data of the tumor-associated changes in an individual GI cancer patient with malignancy. With the introduction of gene panels including next-generation sequencing, it has become possible to identify a variety of mutations and genetic biomarkers in GI cancer. Although the genomic aberration of GI cancer is apparently less actionable compared to other solid tumors, novel informative analyses derived from comprehensive gene profiling may lead to the discovery of precise molecular targeted drugs. These progressions will make it feasible to incorporate clinical, genome-based, and phenotype-based diagnostic and therapeutic approaches and apply them to individual GI cancer patients for precision medicine.     

Proteomic strategies and their application in cancer research

The understanding of carcinogenesis and tumor progression on a molecular basis needs a detailed study of proteins as effector molecules and as critical components of the multiple interconnected signaling pathways that drive the neoplastic phenotype. Thus, the proteomic approach represents a powerful tool for the challenge of the post-genomic era. The term "cancer proteome" refers to the collection of proteins expressed by a given cancer cell and should be considered as a highly dynamic entity within the cell, which affects a variety of cellular activities. The emerging proteomic analysis platforms including 2D-PAGE, mass spectrometry technologies, and protein microarrays represent powerful tools to study and understand cancer. These systems aim to not only identify, catalogue, and characterize cancer proteins, but also to unveil how they interact to affect overall tumor progression. Moreover, recent studies on various cancers have reported promising results concerning the detection of novel molecular biomarkers useful in the early diagnosis of cancer and in drug discovery. Thus, a new subdiscipline named clinical proteomics, concomitant with new molecular technologies that are developed, demonstrates promise to discover new cancer biomarkers. The early diagnosis of cancer, even in a premalignant state, is crucial for the successful treatment of this disease. For these reasons, it is clear that the identification of biomarkers for the early diagnosis of cancer should represent one of the main goals of this emerging field of study.     

Proteoglycans and their functions in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is a highly malignant disease that has a poor prognosis. Its high lethality is mainly due to the lack of symptoms at early stages, which culminates in diagnosis at a late stage when the tumor has already metastasized. Unfortunately, the common cancer biomarkers have low sensitivity and specificity in esophageal cancer. Therefore, a better understanding of the molecular mechanisms underlying ESCC progression is needed to identify novel diagnostic markers and therapeutic targets for intervention. The invasion of cancer cells into the surrounding tissue is a crucial step for metastasis. During metastasis, tumor cells can interact with extracellular components and secrete proteolytic enzymes to remodel the surrounding tumor microenvironment. Proteoglycans are one of the major components of extracellular matrix. They are involved in multiple processes of cancer cell invasion and metastasis by interacting with soluble bioactive molecules, surrounding matrix, cell surface receptors, and enzymes. Apart from having diverse functions in tumor cells and their surrounding microenvironment, proteoglycans also have diagnostic and prognostic significance in cancer patients. However, the functional significance and underlying mechanisms of proteoglycans in ESCC are not well understood. This review summarizes the proteoglycans that have been studied in ESCC in order to provide a comprehensive view of the role of proteoglycans in the progression of this cancer type. A long term goal would be to exploit these molecules to provide new strategies for therapeutic intervention.     

Oncopeptidomics--a commentary on opportunities and limitations

Cancer cells exhibit specific changes in protein expression and alterations in proteolytic activities. Peptides are capable of reflecting these pathological changes and are educible by dedicated analytical technologies. Oncopeptidomics can be defined as the comprehensive multiplexed analysis of endogenous peptides from a biological sample, under defined conditions, to discover probable valid peptide tumor biomarker. Here, mass spectrometry has shown its potential as a comprehensive peptide profiling tool. The efforts to arrive at diagnostically relevant biomarkers may have been underestimated. The establishment of novel cancer biomarkers will necessitate a multidisciplinary effort and presumably require a duration comparable to the drug development process. This review will address current concepts, new perspectives and the developmental process leading to clinically useful peptide tumor markers.     

Using translational research to tailor the use of chemotherapy in the treatment of NSCLC

The treatment of advanced non-small-cell lung cancer (NSCLC) has improved over the past two decades with the availability of new agents such as gemcitabine, the taxanes and vinorelbine. Despite these advances, survival prospects remain disappointingly low for most patients. Further improvements in response rate and survival requires the development of new agents with novel mechanisms of action, such as molecularly targeted therapies, which are currently being tested in clinical trials. The conventional treatment approach to NSCLC is beginning to shift towards the application of specific strategies and techniques, such as pharmacogenomics, to tailor treatment to individual patients. Many efforts are in progress to identify the clinical predictors of outcome. The discovery of prognostic molecular markers, such as the putative suppressor gene (RRM1), represents a novel and potential parameter to help guide clinical treatment decisions.     

Proteomics of gliomas: initial biomarker discovery and evolution of technology

Gliomas are a group of aggressive brain tumors that diffusely infiltrate adjacent brain tissues, rendering them largely incurable, even with multiple treatment modalities and agents. Mostly asymptomatic at early stages, they present in several subtypes with astrocytic or oligodendrocytic features and invariably progress to malignant forms. Gliomas are difficult to classify precisely because of interobserver variability during histopathologic grading. Identifying biological signatures of each glioma subtype through protein biomarker profiling of tumor or tumor-proximal fluids is therefore of high priority. Such profiling not only may provide clues regarding tumor classification but may identify clinical biomarkers and pathologic targets for the development of personalized treatments. In the past decade, differential proteomic profiling techniques have utilized tumor, cerebrospinal fluid, and plasma from glioma patients to identify the first candidate diagnostic, prognostic, predictive, and therapeutic response markers, highlighting the potential for glioma biomarker discovery. The number of markers identified, however, has been limited, their reproducibility between studies is unclear, and none have been validated for clinical use. Recent technological advancements in methodologies for high-throughput profiling, which provide easy access, rapid screening, low sample consumption, and accurate protein identification, are anticipated to accelerate brain tumor biomarker discovery. Reliable tools for biomarker verification forecast translation of the biomarkers into clinical diagnostics in the foreseeable future. Herein we update the reader on the recent trends and directions in glioma proteomics, including key findings and established and emerging technologies for analysis, together with challenges we are still facing in identifying and verifying potential glioma biomarkers.     

Cancer biomarkers: knowing the present and predicting the future

In recent years the discovery of cancer biomarkers has become a major focus of cancer research. The widespread use of prostate-specific antigen in prostate cancer screening has motivated researchers to identify suitable markers for screening different types of cancer. Biomarkers are also useful for diagnosis, monitoring disease progression, predicting disease recurrence and therapeutic treatment efficacy. With the advent of new and improved genomic and proteomic technologies such as DNA and tissue microarray, two-dimensional gel eletrophoresis, mass spectrometry and protein assays coupled with advanced bioinformatic tools, it is possible to develop biomarkers that are able to reliably and accurately predict outcomes during cancer management and treatment. In years to come, a serum or urine test for every phase of cancer may drive clinical decision making, supplementing or replacing currently existing invasive techniques.     

Use of high density antibody arrays to validate and discover cancer serum biomarkers

Perhaps the greatest barrier to translation of serum biomarker discoveries is the inability to evaluate putative biomarkers in high throughput validation studies. Here we report on the development, production, and implementation of a high-density antibody microarray used to evaluate large numbers of candidate ovarian cancer serum biomarkers. The platform was shown to be useful for evaluation of individual antibodies for comparative analysis, such as with disease classification, and biomarker validation and discovery. We demonstrate its performance by showing that known tumor markers behave as expected. We also identify several promising biomarkers from a candidate list and generate hypotheses to support new discovery studies.     

Translational studies for target-based drugs

The biological background for the clinical and prognostic heterogeneity among tumors within the same histological subgroup is due to individual variations in the biology of tumors. The number of investigations looking at the application of novel technologies within the setting of clinical trials is increasing. The most promising way to improve cancer treatment is to build clinical research strategies on intricate biological evidence. New genomic technologies have been developed over recent years. These techniques are able to analyze thousands of genes and their expression profiles simultaneously. The purpose of this approach is to discover new cancer biomarkers, to improve diagnosis, predict clinical outcomes of disease and response to treatment, and to select new targets for novel agents with innovative mechanisms of action. Gene expression profiles are also used to assist in selecting biomarkers of pharmacodynamic effects of drugs in the clinical setting. Biomarker monitoring in surrogate tissues may allow researchers to assess "proof of principle" of new treatments. Clinical studies of biomarkers monitoring toxicity profiles have also been done. Such pharmacodynamic markers usually respond to treatment earlier than clinical response, and as such may be useful predictors of efficacy. Epidermal growth factor receptor (EGFR) mutation in lung cancer tissues is a strong predictive biomarker for EGFR-targeted protein tyrosine kinase inhibitors. Monitoring of EGFR mutation has been broadly performed in retrospective and prospective clinical studies. However, global standardization for the assay system is essential for such molecular correlative studies. A more sensitive assay for EGFR mutation is now under evaluation for small biopsy samples. Microdissection for tumor samples is also useful for the sensitive detection of EGFR mutation. Novel approaches for the detection of EGFR mutation in other clinical samples such as cytology, pleural effusion and circulating tumor cells are ongoing.     

Circulating Biomarkers for Therapeutic Monitoring of Anti-cancer Agents

Circulating biomarkers have emerged as valuable surrogates for evaluating disease states in solid malignancies. Their relative ease of access and rapid turnover has bolstered clinical applications in monitoring treatment efficacy and cancer progression. In this review, the roles of various circulating biomarkers in monitoring treatment response are described. Non-specific markers of disease burden, tumor markers (eg CA 125, CEA, PSA, etc.), circulating tumor cells, nucleic acids, exosomes, and metabolomic arrays are highlighted. Specifically, the discovery of each of these markers is reviewed, with examples illustrating their use in influencing treatment decisions, and barriers to their application noted where these exist. Finally, opportunities for future work using these circulating biomarkers are discussed.     

Blood biomarkers for prostate cancer detection and prognosis

Prostate cancer is the most non-cutaneous malignancy diagnosed in men in the USA. The discovery of prostate-specific antigen (PSA) revolutionized prostate cancer diagnosis and management in the 1990s. Despite its remarkable performance as a marker for prostate cancer, PSA is not prostate cancer specific. PSA can be released by normal as well as hyperplastic prostate cells, which undermines the specificity of PSA for prostate cancer diagnosis. Hence, there is a need for new biomarkers that can detect prostate cancer and, in addition, distinguish indolent from biologically aggressive cancers. Moreover, the emergence of new therapeutic approaches for prostate cancer cannot flourish without a more reliable set of markers to serve as prognosticators, targets and surrogate end points of disease progression and response to treatment. As the most useful clinical biomarkers are likely to be those assayed from blood, there is an increasing interest in profiling blood proteins. With recent advances in biotechnology such as high-throughput molecular analyses, many potential blood biomarkers have been identified and are currently under investigation.     

Breast cancer classification by proteomic technologies: Current state of knowledge

Breast cancer is traditionally considered as a heterogeneous disease. Molecular profiling of breast cancer by gene expression studies has provided us an important tool to discriminate a number of subtypes. These breast cancer subtypes have been shown to be associated with clinical outcome and treatment response. In order to elucidate the functional consequences of altered gene expressions related to each breast cancer subtype, proteomic technologies can provide further insight by identifying quantitative differences at the protein level. In recent years, proteomic technologies have matured to an extent that they can provide proteome-wide expressions in different clinical materials. This technology can be applied for the identification of proteins or protein profiles to further refine breast cancer subtypes or for discovery of novel protein biomarkers pointing towards metastatic potential or therapy resistance in a specific subtype. In this review, we summarize the current state of knowledge of proteomic research on molecular breast cancer classification and discuss important aspects of the potential usefulness of proteomics for discovery of breast cancer-associated protein biomarkers in the clinic.     

代谢组学方法分析肺癌患者血清和尿液小分子代谢产物的初步研究

背景与目的肺癌是当今世界各国最常见的恶性肿瘤之一。目前尚没有寻找到理想的用于肺癌诊断的肿瘤标志物,因而尝试用各种新方法来探索新的生物学标志物已成为肺癌研究的热点。本研究采用代谢组学技术对肺癌患者和其它肺部疾病患者血清及尿液中的小分子代谢物质进行分析,以寻求潜在的肺癌肿瘤标志物。方法运用气相色谱/质谱法(gas chromatography/mass spectrometry,GC/MS)对19例肺癌与15例其它肺部疾病患者的血清及尿液样本进行代谢组学分析,采用正交偏最小二乘判别分析法(orthogonal to partial least squares discriminant analysis,OPLS-DA)进行建模,运用两样本的t检验寻找两组间差异性代谢产物。结果检测到血清中代谢产物共57种,尿液中代谢产物共38种,多变量统计结果显示肺癌患者与其它肺部疾病患者的代谢谱有明显差异,根据t检验结果寻找到血清相关的差异代谢产物13种,尿液相关的差异代谢产物7种。结论利用代谢组学方法能区分肺癌与其它肺部疾病患者,其结果在分子水平辅助肺癌的诊断、未来作为新技术应用于肺癌的诊断有一定的前景。     

Testicular Cancer Biomarkers: A Role for Precision Medicine in Testicular Cancer

Testicular germ cell tumors (TGCTs) represent the most common solid tumors among men aged 15 to 34 years. Fortunately, recent advances have made testicular cancer a highly curable disease. Despite the high cure rates, there are still several areas in testis cancer care where treatment decisions are controversial and guided only with clinical factors and historic serum tumor markers. Unfortunately, unlike other genitourinary malignancies, modern research techniques have not been widely tested or applied to germ cell tumors, perhaps as a result of excellent prognosis in this cohort of young men. Despite this, there remain numerous challenges and pitfalls in testis cancer care that need to be addressed.A reliable set of biomarkers could be extremely useful in helping risk-stratify patients, detect relapse early, guide surgical decision-making, and tailor follow-up.Current tumor markers (Alpha-fetoprotein, human chorionic gonadotrophin, and lactate dehydrogenase) have low accuracy and low sensitivity when used not only as diagnostic but also as prognostic and predictive markers. In twenty-first century medicine, there is a role for further prognostic stratification and the development of novel biomarkers that offer greater sensitivity and specificity for TGCTs. Despite the initial promising results, the majority of preclinical biomarkers do not, as yet have a proven validated role in clinical practice, and future prospective trials are needed to support and confirm the results of cohort studies.In this narrative review, we aimed to highlight the recent innovations in the development and implementation of novel testicular tumor markers and discuss their clinical applications and limitations in the management of this disease.     

Translational crossroads for biomarkers.

A group of investigators met at a Specialized Programs of Research Excellence Workshop to discuss key issues in the translation of biomarker discovery to the development of useful laboratory tests for cancer care. Development and approval of several new markers and technologies have provided informative examples that include more specific markers for prostate cancer, more sensitive tests for ovarian cancer, more objective analysis of tissue architecture and an earlier indication of response to treatment in breast cancer. Although there is no clear paradigm for biomarker development, several principles are clear. Marker development should be driven by clinical needs, including early cancer detection, accurate pretreatment staging, and prediction of response to treatment, as well as monitoring disease progression and response to therapy. Development of a national repository that uses carefully preserved, well-annotated tissue specimens will facilitate new marker development. Reference standards will be an essential component of this process. Both hospital-based and commercial laboratories can play a role in developing biomarkers from discovery to test validation. Partnering of academe and industry should occur throughout the process of biomarker development. The National Cancer Institute is in a unique position to bring together academe, industry, and the Food and Drug Administration to (a) define clinical needs for biomarkers by tumor type, (b) establish analytic and clinical paradigms for biomarker development, (c) discuss ways in which markers from different companies might be evaluated in combination, (d) establish computational methods to combine data from multiple biomarkers, (e) share information regarding promising markers developed in National Cancer Institute-supported programs, and (f) exchange data regarding new platforms and techniques that can accelerate marker development.