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Concentrating on molecular biomarkers in cancer research, Cancer Biomarkers publishes original research findings (and reviews solicited by the editor) on the subject of the identification of markers associated with the disease processes whether or not they are an integral part of the pathological lesion.
The disease markers may include, but are not limited to, genomic, epigenomic, proteomics, cellular and morphologic, and genetic factors predisposing to the disease or indicating the occurrence of the disease. Manuscripts on these factors or biomarkers, either in altered forms, abnormal concentrations or with abnormal tissue distribution leading to disease causation will be accepted.
Authors: Cole, Kimberly | Tabernero, Maria | Anderson, Karen S.
Article Type: Research Article
Abstract: Breast cancer is the second leading cause of cancer death in women in the United States. While mammography and breast magnetic resonance imaging (MRI) improve detection of early disease, there remains an unmet need for biomarkers for risk stratification, early detection, prediction, and disease prognosis. A number of early breast lesions, from atypical hyperplasias to carcinomas in situ, are associated with an increased risk of developing subsequent invasive breast carcinoma. The recent development of genomic, epigenomic, and proteomic tools for tissue biomarker detection, including array CGH, RNA expression microarrays, and proteomic arrays have identified a number of potential biomarkers that …both identify patients at increased risk, as well as provided insights into the pathology of early breast cancer development. This chapter focuses on the detection and application of tissue and serum biomarkers for the identification and risk stratification of early breast cancer lesions. Show more
Keywords: Breast cancer, benign breast disease, biomarkers
DOI: 10.3233/CBM-2011-0187
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 177-192, 2011
Authors: Adamson, D. Cory | Rasheed, B. Ahmed K. | McLendon, Roger E. | Bigner, Darell D.
Article Type: Research Article
Abstract: Several different types of tumors, benign and malignant, have been identified in the central nervous system (CNS). The prognoses for these tumors are related to several factors, such as the age of the patient and the location and histology of the tumor. In adults, about half of all CNS tumors are malignant, whereas in pediatric patients, more than 75% are malignant. For most benign CNS tumors that require treatment, neurosurgeons can offer curative resections or at least provide significant relief from mass effect. Unfortunately, we still lack effective treatments for most primary and secondary malignant CNS tumors. However, the past …decade has witnessed an explosion in the understanding of the early molecular events in malignant primary CNS tumors, and for the first time in history, oncologists are seeing that a plethora of new therapies targeting these molecular events are being tested in clinical trials. There is hope on the horizon for the fight against these deadly tumors. The distribution of CNS tumors by location has remained constant for numerous years. The majority of primary CNS tumors arise in the major cortical lobes. Twenty nine percent of primary CNS tumors arise from the dural meninges that encase the CNS structures. The vast majority of these are meningiomas, of which over 90% are benign. About 10% of primary CNS tumors are found in the sella turcica region, where the pituitary gland resides. Other much less common sites of primary CNS tumors include the pineal region, ventricular system, cerebellum, brain stem, cranial nerves, and spinal cord. The distribution of CNS tumors by histology has seen a slight increase in more malignant tumors over the past decade, possibly due to increased neuroimaging practices or environmental exposures. Arising from glial cells, gliomas represent over 36% of all primary CNS tumors and consist of astrocytomas, oligodendrogliomas, ependymomas, mixed gliomas, and neuroepithelial tumors. The benign meningiomas make up 32% of primary CNS tumors, followed by nerve sheath tumors and pituitary tumors. Primary CNS lymphomas, embryonal tumors, and craniopharyngiomas are uncommon. The most common gliomas are astrocytomas, and these tumors are typically classified by the World Health Organization (WHO) as Grades I through IV. Grade IV, the most malignant grade of astrocytoma, includes glioblastoma multiforme (GBM), the most common malignant primary CNS glioma in adults, which represents 51% of all CNS gliomas. GBM is unfortunately the most challenging to effectively treat and has the worst patient survival. This chapter is therefore primarily devoted to the current understanding of this topic. Here we describe the molecular and cellular events associated with malignant glioma initiation and progression. We also review the importance of glioma stem cell biology and tumor immunology in early gliomagenesis. In addition, we present a brief description of the most common malignant primary CNS glioma in pediatric patients – medulloblastoma, as well as familial cancer syndromes that include gliomas as part of the syndrome. Show more
Keywords: Central nervous system, brain, glioma, astrocytoma, glioblastoma, glioblastoma multiforme, GBM, oligodendroglioma, medulloblastoma, EGFR, EGFRvIII, MGMT, PTEN, TP53, VEGF, PDGFR, TGF-b, Myc, Otx2, PTCH, glioma stem cell, CD133, Olig2
DOI: 10.3233/CBM-2011-0177
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 193-210, 2011
Authors: Rushton, Jennifer | López-Terrada, Dolores
Article Type: Research Article
Abstract: Pediatric malignancies are a spectrum of biologically diverse cancers different from those seen in adults. Malignant solid tumors diagnosed in children are often, and at least partly the result of developmental pathways dysregulation, and may recapitulate stages of organogenesis. Significant insight into their pathogenesis came from studying normal embryonal and fetal organ development, as well as mechanisms responsible for developmental disorders and congenital syndromes associated with these tumors. Systematic integration of pathology, genetic and molecular analyses of pediatric solid tumors is allowing the recognition of distinct clinical tumor subtypes, as well as potential therapeutic targets for some of …these neoplasms. From the diagnostic point of view, some pediatric solid tumors represent examples of clinical translation, as genetic and molecular markers are being incorporated into clinical algorithms, and used for tumor classification, risk stratification, theragnostics or disease monitoring. The on-going comprehensive analysis of some pediatric tumor types using genomic, expression and epigenetic profiling technologies, and the development of experimental tumor model systems, are fastly improving our understanding of their biology. However, further and comprehensive characterization of other pediatric solid tumors, particularly aggressive or chemoresistant cancer types, is still necessary, and should result in the development of new integrated clinical testing, improved therapeutic strategies and better outcomes for these patients. Show more
Keywords: Childhood, cancer, molecular, genetic, pathology, tumor markers, embryonal tumors, developmental pathways, profiling, epigenetics, risk stratification, molecular diagnostics, prognosis
DOI: 10.3233/CBM-2011-0199
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 211-234, 2011
Authors: Manne, Upender | Shanmugam, Chandrakumar | Katkoori, Venkat R. | Bumpers, Harvey L. | Grizzle, William E.
Article Type: Research Article
Abstract: A variety of genetic and molecular alterations underlie the development and progression of colorectal neoplasia (CRN). Most of these cancers arise sporadically due to multiple somatic mutations and genetic instability. Genetic instability includes chromosomal instability (CIN) and microsatellite instability (MSI), which is observed in most hereditary non-polyposis colon cancers (HNPCCs) and accounts for a small proportion of sporadic CRN. Although many biomarkers have been used in the diagnosis and prediction of the clinical outcomes of CRNs, no single marker has established value. New markers and genes associated with the development and progression of CRNs are being discovered at an accelerated …rate. CRN is a heterogeneous disease, especially with respect to the anatomic location of the tumor, race/ethnicity differences, and genetic and dietary interactions that influence its development and progression and act as confounders. Hence, efforts related to biomarker discovery should focus on identification of individual differences based on tumor stage, tumor anatomic location, and race/ethnicity; on the discovery of molecules (genes, mRNA transcripts, and proteins) relevant to these differences; and on development of therapeutic approaches to target these molecules in developing personalized medicine. Such strategies have the potential of reducing the personal and socio-economic burden of CRNs. Here, we systematically review molecular and other pathologic features as they relate to the development, early detection, diagnosis, prognosis, progression, and prevention of CRNs, especially colorectal cancers (CRCs). Show more
Keywords: Early detection, molecular diagnosis, prognosis, molecular staging, colorectal cancer
DOI: 10.3233/CBM-2011-0160
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 235-265, 2011
Authors: Bogenrieder, Thomas | Herlyn, Meenhard
Article Type: Research Article
Abstract: Cutaneous melanoma is a highly aggressive cancer with still limited, but increasingly efficacious, standard treatment options. Recent preclinical and clinical findings support the notion that cutaneous melanoma is not one malignant disorder but rather a family of distinct molecular diseases. Incorporation of genetic signatures into the conventional histopathological classification of melanoma already has great implications for the management of cutaneous melanoma. Herein, we review our rapidly growing understanding of the molecular biology of cutaneous melanoma, including the pathogenic roles of the mitogen-associated protein kinase (MAPK) pathway, the phosphatidylinositol 3 kinase [PI3K]/phosphatase and tensin homologue deleted on chromosome 10 [PTEN]/Akt/mammalian target …of rapamycin [mTOR])PTEN (phosphatase and tensin homolog) pathway, MET (hepatocyte growth factor), Notch signaling, and other key molecules regulating cell cycle progression and apoptosis. The mutation Val600Glu in the BRAF oncogene (designated BRAF(V600E)) has been associated with clinical benefit from agents that inhibit BRAF(V600E) or MEK (a kinase in the MAPK pathway). Cutaneous melanomas arising from mucosal, acral, chronically sun-damaged surfaces sometimes have oncogenic mutations in KIT, against which several inhibitors have shown clinical efficacy. These findings suggest that prospective genotyping of patients with melanoma, combined with the growing availability of targeted agents, which can be used to rationally exploit these findings, should be used increasingly as we work to develop new and more effective treatments for this devastating disease. Show more
Keywords: Melanoma, cell cycle, pRb pathway, p16INK4A, p14ARF, cyclins, CDKs, Apaf1, Bcl2, MAPK pathway, Ras, BRAF, PTEN, PI3K/AKTpathway, SCF, ckit, HGF, cmet, cmyc, Notch
DOI: 10.3233/CBM-2011-0164
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 267-286, 2011
Authors: Merritt, Melissa A. | Cramer, Daniel W.
Article Type: Research Article
Abstract: Pregnancy, breastfeeding, and oral contraceptive pill use interrupt menstrual cycles and reduce endometrial and ovarian cancer risk. This suggests the importance of turnover within Mullerian tissues, where the accumulation of mutations in p53 and PTEN has been correlated with number of cycles. The most common type of endometrial cancer (Type I) is endometrioid and molecular abnormalities include mutations in PTEN, KRAS and β-catenin. The Type I precursor is Endometrial Intraepithelial Neoplasia which displays PTEN defects. Type II endometrial cancer (whose precursors are less clear) includes serous and clear cell tumors and the most common alteration is p53 mutation. For ovarian …cancer, histopathologic types parallel endometrial cancer and include serous, mucinous, endometrioid, and clear cell; some molecular features are also shared. The most frequent type of ovarian cancer is high grade serous that often displays p53 mutation and its precursor lesions may originate from normal-appearing fallopian tube epithelium that contains a p53 “signature”. Mutations in KRAS, BRAF and PTEN are described in mucinous, endometrioid and low grade serous cancers and these may originate from ovarian cortical inclusion cysts. A consideration of molecular and other pathogenetic features, like epidemiology and histopathology, may provide a better understanding of endometrial and ovarian cancer. Show more
Keywords: Ovarian cancer, Endometrial cancer, p53, PTEN, KRAS, Precursor lesions, Endometrial intraepithelial neoplasia, Fallopian tube, Cortical inclusion cysts, mullerian, epidemiology, risk factors, Type I, Type II, serous, mucinous, endometrioid, clear cell
DOI: 10.3233/CBM-2011-0167
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 287-305, 2011
Authors: Reid, Brian J.
Article Type: Research Article
Abstract: Barrett’s esophagus is a condition in which the stratified squamous epithelium of the distal esophagus is replaced by specialized intestinal metaplasia. Clinical management of Barrett’s esophagus, like many other “premalignant” conditions, is characterized by overdiagnosis of benign early changes that will not cause death or suffering during the lifetime of an individual and underdiagnosis of life-threatening early disease. Recent studies of a number of different types of cancer have revealed much greater genomic complexity than was previously suspected. This genomic complexity could create challenges for early detection and prevention if it develops in premalignant epithelia prior to cancer. Neoplastic progression …unfolds in space and time, and Barrett’s esophagus provides one of the best models for rapid advances, including “gold standard” cohort studies, to distinguish individuals who do and do not progress to cancer. Specialized intestinal metaplasia has many properties that appear to be protective adaptations to the abnormal environment of gastroesophageal reflux. A large body of evidence accumulated over several decades implicates chromosome instability in neoplastic progression from Barrett’s esophagus to esophageal adenocarcinoma. Small, spatial scale studies have been used to infer the temporal order in which genomic abnormalities develop during neoplastic progression in Barrett’s esophagus. These spatial studies have provided the basis for prospective cohort studies of biomarkers, including DNA content abnormalities (tetraploidy, aneuploidy) and a biomarker panel of 9p LOH, 17p LOH and DNA content abnormalities. Recent advances in SNP array technology provide a uniform platform to assess chromosome instability. Show more
Keywords: Barrett’s esophagus, esophageal adenocarcinoma, clonal evolution, genome instability, chromosome instability, aneuploidy, biomarkers, SNP arrays, telomeres, nonsteroidal anti-inflammatory drugs, genetic diversity, clonal expansion, hitchhikers ("passengers"), gastroesophageal reflux disease (GERD), dysplasia, Peter Nowell
DOI: 10.3233/CBM-2011-0162
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 307-324, 2011
Authors: Park, Brian J. | Chiosea, Simion I. | Grandis, Jennifer R.
Article Type: Research Article
Abstract: Head and neck squamous cell carcinomas (SCCHN) arise in the mucosa of the upper aerodigestive tract at multiple anatomic sites. While tobacco and alcohol exposure remain the primary risk factors for this malignancy, infection with the human papilloma virus is emerging as a major contributing factor to cancers that arise primarily in the oropharynx. Despite therapeutic advances, survival has remained relatively unchanged over the past few decades. Increased understand of the cellular and molecular biology of these cancers will improve our understanding of this malignancy and facilitate the development of more effective therapeutic strategies. Alterations that have been studied to …date include genetic and epigenetic changes. While the epidermal growth factor receptor (EGFR) is the only established molecular therapeutic target, other proteins and pathways are under active investigation to determine their contribution to SCCHN carcinogenesis and progression. Show more
Keywords: Head and neck cancer, molecular pathogenesis, squamous cell carcinoma, leukoplakia, premalignant, human papilloma virus
DOI: 10.3233/CBM-2011-0163
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 325-339, 2011
Authors: Zhao, X. Frank | Reitz, Marvin | Chen, Qing Ching | Stass, Sanford
Article Type: Research Article
Abstract: In the past several decades, great progress has been made in our understanding of normal hematopoiesis and its malignant transformation. This article provides a comprehensive and up-to-date review of pathogenesis of leukemia and lymphoma, with an emphasis on early molecular events. Current concepts of normal hematopoiesis and its key regulatory processes are summarized. Various environmental and infectious factors that play a causative role in hematopoietic malignancies are described. In particular, several causative viruses, i.e. HTLV1, HHV8 and EBV, are discussed in depth. Numerous genetic abnormalities have been identified in leukemia and lymphoma, including chromosomal translocations, gene deletions, amplifications, and point …mutations. Synopses are included for the most frequently encountered aberrations, and their relation to normal and malignant hematopoiesis, disease classification and prognosis. Major molecular mechanisms and signal transduction pathways involved in the leukemogenesis are depicted; these include blockage of differentiation, self-sustainable proliferation, abnormal cell cycle progression and impaired apoptosis. Also included are the recently discovered microRNAs, and their potential role in the pathogenesis of leukemia and lymphoma. Future directions in leukemia and lymphoma research are presented, including several modern molecular technologies and their importance in developing new biomarkers for early detection of leukemia and lymphoma. Show more
Keywords: Leukemia, lymphoma, hematopoiesis, stem cells, pathogenesis, leukemogenesis, chromosomal translocation, Philadelphia chromosome, oncogene, tumor suppressor, microRNA, retrovirus, herpes virus, acute myeloid leukemia, acute lymphoblastic leukemia, chronic myeloproliferative neoplasm, gene expressing profiling
DOI: 10.3233/CBM-2011-0178
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 341-374, 2011
Authors: Block, Timothy | Mehta, Anand S. | London, W. Thomas
Article Type: Research Article
Abstract: Primary cancer of the liver, hepatocellular carcinoma (HCC), is an extremely deadly cancer, with very poor 5 year survivals, following diagnosis. The poor outcomes are believed to be due, in part, to the late times in which the cancers are usually first detected. Improved methods for early detection have thus become a top priority in the management of liver cancer. This Chapter reviews current methods of detection as well as leading new methods. Possible explanations as to why there are so many markers that are being discovered, but so few that make it to validation are discussed.
Keywords: Liver Cancer, Hepatocellular carcinoma, hepatitis B, hepatitis C, early detection, early diagnosis, biomarkers
DOI: 10.3233/CBM-2011-0165
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 375-383, 2011
Authors: Gazdar, Adi F. | Brambilla, Elisabeth
Article Type: Research Article
Abstract: As with other epithelial cancers, lung cancer develops over a period of several years or decades via a series of progressive morphological changes accompanied by molecular alterations that commence in histologically normal epithelium. However the development of lung cancer presents certain unique features that complicates this evaluation. Anatomically the respiratory tree may be divided into central and peripheral compartments having different gross and histological anatomies as well as different functions. In addition, there are three major forms of lung cancer and many minor forms. Many of these forms arise predominantly in either the central or peripheral compartments. Squamous cell and …small cell carcinomas predominantly arise in the central compartment, while adenocarcinomas predominantly arise peripherally. Large cell carcinomas are not a single entity but consist of poorly differentiated forms of the other types and, possibly, some truly undifferentiated “stem cell like” tumors. The multistage origin of squamous cell carcinomas, because of their central location, can be followed more closely than the peripherally arising adenocarcinomas. Squamous cell carcinomas arise after a series of reactive, metaplastic, premalignant and preinvasive changes. However, long term observations indicate that not all tumors follow a defined histologic course, and the clinical course, especially of early lesions, is difficult to predict. Peripheral adenocarcinomas are believed to arise from precursor lesions known as atypical adenomatous hyperplasias and may have extensive in situ growth before becoming invasive. Small cell carcinomas are believed to arise from severely molecularly damaged epithelium without going through recognizable preneoplastic changes. The molecular changes that occur prior to the onset on invasive cancers are extensive. As documented in this chapter, they encompass all of the six classic Hallmarks of Cancer other than invasion and metastasis, which by definition occur beyond preneoplasia. A study of preinvasive lung cancer has yielded much valuable biologic information that impacts on clinical management. Show more
Keywords: Lung cancer, squamous cell carcinoma, adenocarcinomas, small cell lung carcinoma, preneoplasia, carcinoma in situ, atypical adenomatous hyperplasia, tumor suppressor genes, oncogenes, apoptosis, telomerase, angiogenesis
DOI: 10.3233/CBM-2011-0166
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 385-396, 2011
Authors: Balic, Marija | Williams, Anthony | Dandachi, Nadia | Cote, Richard J.
Article Type: Research Article
Abstract: Metastatic disease is the most important determinant in the clinical management of patients with cancer. Disseminated tumor cells are regarded as a surrogate for early metastatic spread of disease. These cells can be detected in bone marrow aspirates, lymph nodes and peripheral blood, where we refer to them as circulating tumor cells. Detection of disseminated tumor cells represents a great technical challenge, and many different technologies have been developed to enhance the sensitivity and specificity of the testing for these rare events. Different characteristics of tumor cells have been used to establish enrichment methods, including the differential expression of tumor-specific …markers on the surface of the cells, the size-based selection of the cells, and other physical properties. Despite technical obstacles, the detection of circulating tumor cells in particular have emerged in recent years as a biomarker with outstanding predictive and prognostic capacity in a number of malignancies including breast, prostate, lung and colorectal cancer. In this text, we provide a comprehensive review of different approaches for enrichment of disseminated and circulating tumor cells and elucidate additional molecular methods for their detection. Further, the clinical significance of disseminated tumor cells detected in various compartments is discussed. Based on recent findings on the biology and heterogeneity of tumor cells, along with development of robust enrichment techniques, we believe that future research will focus less on pure detection but more importantly on detailed molecular characterization of these rare events with the potential impact on design of novel therapeutics. Show more
Keywords: Metastasis, circulating tumor cells (CTC), disseminated tumor cells (DTC), CTC enrichment, membrane microfilter device, microfiltration, cancer stem cells, breast cancer, prostate cancer, colorectal cancer, bladder cancer
DOI: 10.3233/CBM-2011-0161
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 397-419, 2011
Authors: Remmers, Neeley | Bailey, Jennifer M. | Mohr, Ashley M. | Hollingsworth, Michael A.
Article Type: Research Article
Abstract: We describe the pathology of early pancreatic cancer and present an overview of known molecular alterations that occur in these lesions. There are three defined precursor lesions in current models of pancreatic cancer: pancreatic intraepithelial neoplasia (PanIN), mucinous cystic neoplasms (MCN), and intraductal papillary mucinous neoplasms (IPMN). Molecular alterations detected in these lesions include: telomeres, K-ras and downstream targets, p16/CDKN2A, p53, SMAD4/DPC4, microRNAs, mucins and their post-translational processing, inflammatory cytokines, CEACAM, and epigenetic alterations. We summarize previous analyses of these markers as diagnostic markers of disease, and suggest areas of future study.
Keywords: Pancreatic cancer, pancreatic intraepithelial neoplasia (PanIN), mucinous cystic neoplasms (MCN), intraductal papillary mucinous neoplasms (IPMN), mucin, K-ras, p16/CDKN2A, p53, SMAD4/DPC4, microRNA, CEACAM, MIC1, CA19-9
DOI: 10.3233/CBM-2011-0168
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 421-440, 2011
Authors: Cazares, L.H. | Drake, R.R. | Esquela-Kirscher, A. | Lance, R.S. | Semmes, O.J. | Troyer, D.A.
Article Type: Research Article
Abstract: This chapter includes discussion of the molecular pathology of tissue, blood, urine, and expressed prostatic secretions. Because we are unable to reliably image the disease in vivo, a 12 core method that oversamples the peripheral zone is widely used. This generates large numbers of cores that need to be carefully processed and sampled. In spite of the large number of tissue cores, the amount of tumor available for study is often quite limited. This is a particular challenge for research, as new biomarker assays will need to preserve tissue architecture intact for histopathology. Methods of processing and reporting pathology are …discussed. With the exception of ductal variants, recognized subtypes of prostate cancer are largely confined to research applications, and most prostate cancers are acinar. Biomarker discovery in urine and expressed prostatic secretions would be useful since these are readily obtained and are proximate fluids. The well-known challenges of biomarker discovery in blood and urine are referenced and discussed. Mediators of carcinogenesis can serve as biomarkers as exemplified by mutations in PTEN and TMPRSS2:ERG fusion. The use of proteomics in biomarker discovery with an emphasis on imaging mass spectroscopy of tissues is discussed. Small RNAs are of great interest, however, their usefulness as biomarkers in clinical decision making remains the subject of ongoing research. The chapter concludes with an overview of blood biomarkers such as circulating nucleic acids and tumor cells and bound/free isoforms of prostate specific antigen (PSA). Show more
Keywords: Prostate Cancer, Prostate Pathology, Predictive Biomarkers, Molecular Markers of Cancer, Prostate Histopathology, Cytogenetics and Prostate Cancer, Proteomics and Prostate Cancer, microRNAs and Prostate Cancer, Expressed prostatic secretions and prostate cancer
DOI: 10.3233/CBM-2011-0181
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 441-459, 2011
Authors: Cairns, Paul
Article Type: Research Article
Abstract: Renal Cell Carcinoma (RCC) has the highest mortality rate of the genitourinary cancers and the incidence of RCC has risen steadily. If detected early, RCC is curable by surgery although a minority are at risk of recurrence. Increasing incidental detection and an ageing population has led to active surveillance as an option for patients with small renal masses. RCC is heterogeneous and comprises several histological cell types with different genetics, biology and behavior. The identification of the genes predisposing to inherited syndromes with RCC has provided much of our knowledge of the molecular basis of early sporadic RCC. Many of …the oncogenes and tumor suppressor genes that are mutated leading to pathway dysregulation in RCC remain to be elucidated. Global studies of copy number, gene sequencing, gene expression, miRNA expression and gene methylation in primary RCC will lead towards this goal. The natural history of RCC indicated by candidate precursor lesions, multifocal or bilateral disease, growth rate of small renal masses under surveillance, and high risk populations provide insight into the behavior of this disease. The use of molecular markers for early detection and prognosis merits more attention with ongoing advances in omics technologies. This review focuses on early RCC, that is disease confined within the renal capsule. Show more
Keywords: Renal cell carcinoma (RCC), clear cell, papillary, chromophobe, small renal masses (SRM), genetics, epigenetics, hypermethylation, natural history, precursor lesion, multifocal, end stage renal disease (ESRD), diagnosis, prognosis, therapy
DOI: 10.3233/CBM-2011-0176
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 461-473, 2011
Authors: Powers, Martin | Zhang, Wei | Lopez-Terrada, Dolores | Czerniak, Bogdan A. | Lazar, Alexander J.
Article Type: Research Article
Abstract: Sarcomas are rare malignancies of mesenchymal lineage with more than 100 specific types and many benign potential mimics. In situ and precursor lesions are generally not described and thus much of molecular pathology in this field concentrates on molecular diagnosis, prognosis and determination of therapeutic targets. This chapter discusses the applications of molecular methodologies that provide insight into pathogenesis of sarcoma, and of molecular methods which are currently applied to, or will likely soon influence, the clinical management of this complex array of tumors.
Keywords: Sarcoma, translocation, EWSR1, reverse transcriptase-polymerase chain reaction (RT-PCR), fluoresence in-situ hybridization (FISH), fusion transcript, molecular diagnostics, pigmented villonodular synovitis, Ewing sarcoma, gastrointestinal stromal tumor (GIST), KIT, PDGRA, karyotype, desmoid fibromatosis, beta-catenin (CTNNB1), malignant peripheral nerve sheath tumor (MPNST), leiomyosarcoma, genomic profiling
DOI: 10.3233/CBM-2011-0170
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 475-491, 2011
Authors: David, Stefan | Meltzer, Stephen J.
Article Type: Research Article
Abstract: Gastric cancer is one of the most common neoplasias in the world and remains an important cause of cancer-related mortality. Vast resources have been invested in the study of the molecular events driving the development and progression of gastric tumors. Gastric cancer is known to result from an interaction between host and environmental factors. The present review will discuss the most how genetic and epigenetic changes contribute to gastric carcinogenesis and their potential for developing novel diagnostic and therapeutic tools.
Keywords: Gastric cancer, genetics, epigenetics, microsatellite instabilitychromosomal instability, mutation, deletion, translocation, methylation, oncogene, tumor suppressor gene
DOI: 10.3233/CBM-2011-0169
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 493-507, 2011
Authors: Crichton, Daniel J. | Mattmann, Chris A. | Thornquist, Mark | Anton, Kristen | Hughes, J. Steven
Article Type: Research Article
Abstract: Capturing, sharing, and publishing cancer biomarker research data are all fundamental challenges of enabling new opportunities to research and understand scientific data. Informatics experts from the National Cancer Institute's (NCI) Early Detection Research Network (EDRN) have pioneered a principled informatics infrastructure to capture and disseminate data from biomarker validation studies, in effect, providing a national-scale, real-world successful example of how to address these challenges. EDRN is a distributed, collaborative network and it requires its infrastructure to support research across cancer research institutions and across their individual laboratories. The EDRN informatics infrastructure is also referred to as the EDRN Knowledge Environment, …or EKE. EKE connects information about biomarkers, studies, specimens and resulting scientific data, allowing users to search, download and compare each of these disparate sources of cancer research information. EKE's data is enriched by providing annotations that describe the research results (biomarkers, protocols, studies) and that link the research results to the captured information within EDRN (raw instrument datasets, specimens, etc.). In addition EKE provides external links to public resources related to the research results and captured data. EKE has leveraged and reused data management software technologies originally developed for planetary and earth science research results and has infused those capabilities into biomarker research. This paper will describe the EDRN Knowledge Environment, its deployment to the EDRN enterprise, and how a number of these challenges have been addressed through the capture and curation of biomarker data results. Show more
Keywords: EDRN knowledge environment, data intensive systems, biomarker research, informatics infrastructure, e-science, metadata, data curation, data sharing, biomarker database, Data Grid
DOI: 10.3233/CBM-2011-0180
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 511-530, 2011
Authors: Grizzle, William E. | Bell, Walter C. | Sexton, Katherine C.
Article Type: Research Article
Abstract: The availability of human tissues to support biomedical research is critical to advance translational research focused on identifying and characterizing approaches to individualized (personalized) medical care. Providing such tissues relies on three acceptable models – a tissue banking model, a prospective collection model and a combination of these two models. An unacceptable model is the "catch as catch can" model in which tissues are collected, processed and stored without goals or a plan or without standard operating procedures, i.e., portions of tissues are collected as available and processed and stored when time permits. In the tissue banking model, aliquots of …tissues are collected according to SOPs. Usually specific sizes and types of tissues are collected and processed (e.g., 0.1 gm of breast cancer frozen in OCT). Using the banking model, tissues may be collected that may not be used and/or do not meet specific needs of investigators; however, at the time of an investigator request, tissues are readily available as is clinical information including clinical outcomes. In the model of prospective collection, tissues are collected based upon investigator requests including specific requirements of investigators. For example, the investigator may request that two 0.15 gm matching aliquots of breast cancer be minced while fresh, put in RPMI media with and without fetal calf serum, cooled to 4°C and shipped to the investigator on wet ice. Thus, the tissues collected prospectively meet investigator needs, all collected specimens are utilized and storage of specimens is minimized; however, investigators must wait until specimens are collected, and if needed, for clinical outcome. The operation of any tissue repository requires well trained and dedicated personnel. A quality assurance program is required which provides quality control information on the diagnosis of a specimen that is matched specifically to the specimen provided to an investigator instead of an overall diagnosis of the specimen via a surgical pathology report. This is necessary because a specific specimen may not match the diagnosis of the case due to many factors such as necrosis, unsuspected tumor invasion of apparently normal tissue, and areas of fibrosis which are mistaken grossly for tumor. Aliquots for quality control (QC) may or may not be collected at the time of collection and in some cases, QC may not occur until specimens are distributed to investigators. In establishing a tumor repository, multiple issues need to be considered. These include the available resources, long term support, space and equipment. The needs of the potential users need to be identified as to the types of tissues and services needed and the annotation expected. Other specific issues to be considered include collection of specimens potentially infected with blood borne pathogens (e.g., hepatitis B), charge back mechanisms, informatics needs and support, and investigator requirements (e.g., recognition of repository contributions in publications). In general, the repository should not perform the research of the investigators, but should provide the infrastructure necessary to support the research of the investigator. Thus, the goals of the repository must be established. Similarly, ethical and regulatory issues must be evaluated. In general, tissue repositories need ethical (e.g., IRB) and privacy (e.g., HIPAA) review. Also, safety issues need to be considered as well as how biohazards will be addressed by investigator-users. Considerations involving the transfer of specimens to other organization usually require a material transfer agreement (MTA). A MTA should address biohazards as well as indemnification. Thus, many issues must be considered and addressed in order to establish and operate successfully a biorepository. Show more
Keywords: Tissue repositories, tissue banking, prospective collections, quality control, quality assurance, repository science, bias, clinical trials, epidemiology, annotation, material transfer agreement, shipping, informatics, safety, biohazards, security, difficult requests, caBIG, vocabulary, common data elements, chemical hazards, cost recovery, HIPAA, informed consent, demographics, clinical information, training, audits, good manufacturing practice, storage, specimen identification, services
DOI: 10.3233/CBM-2011-0183
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 531-549, 2011
Article Type: Other
DOI: 10.3233/CBM-2011-91-630
Citation: Cancer Biomarkers, vol. 9, no. 1-6, pp. 551-552, 2011
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