The role of tissue microarrays in prostate cancer biomarker discovery

Tissue microarrays (TMAs) offer the potential to rapidly translate genomics and basic science research findings to practical clinical application. This is particularly true in the field of cancer biomarker research, where TMAs can be used for candidate biomarker validation and association with patient clinical, pathologic, and outcomes parameters. In this review, we examine the effect of TMA use on prostate cancer biomarker research, focusing on the types of TMAs that have been used, and the biomarkers that have been examined. The results demonstrate that TMAs have been very effective in screening candidate biomarkers for subsequent, extended evaluation in large patient populations. In addition, the use of TMAs in multiple biomarker series allows for the statistical analysis of sets of biomarkers as diagnostic or prognostic tests. The processes used here can be applied to any tumor type to improve patient diagnosis, prognosis, and treatment response prediction.     

Beyond PSA: the next generation of prostate cancer biomarkers

Since the introduction of serum prostate-specific antigen (PSA) screening 25 years ago, prostate cancer diagnosis and management have been guided by this biomarker. Yet, PSA has proven controversial as a screening assay owing to several inherent limitations. The next wave of prostate cancer biomarkers has emerged, introducing new assays in serum and urine that may supplement or, in time, replace PSA because of their higher cancer specificity. This expanding universe of biomarkers has been facilitated, in large part, by new genomic technologies that have enabled an unbiased look at cancer biology. Such efforts have produced several notable success stories that involve rapidly moving biomarkers from the bench to the clinic. However, biomarker research has centered on disease diagnostics, rather than prognosis and prediction, which would address disease management. The development of biomarkers to stratify risk of prostate cancer aggressiveness at the time of screening remains the greatest unmet clinical need in prostate cancer. We review the current state of prostate cancer biomarker research, including the PSA revolution, its impact on early cancer detection, the recent advances in biomarker discovery, and the future efforts that promise to improve clinical management of this disease.     

Predictive and prognostic biomarker testing in invasive breast cancer

Surgical pathologists play an important role in ordering and interpreting biomarker testing for prognostic and predictive purposes. In invasive breast cancer, these biomarkers include hormone receptors, HER2 expression, multi-gene expression assays, checkpoint inhibitor staining, single gene mutation status, and genomic findings. Additionally, there are tests that predict response to “tumor-agnostic” drugs targeting gene-specific alterations or protein expression changes, regardless of tumor type. The assays employed to assess these biomarkers range from immunohistochemistry to RNA expression to next-generation sequencing. Each assay has specific indications and technical pitfalls. The pathologist must select the correct specimen, choose the area for microdissection, and consider cellularity and tissue adequacy. Often, the pathologist will also provide interpretation of the results. This review will provide an overview of these biomarker tests in breast cancer, describe their indications and utilization, and list some of their challenges. It will serve as a practical reference for pathologists in their integral role in patient care.     

Cell‐free microRNAs as diagnostic,prognostic, and predictive biomarkers for lung cancer

Lung cancer is the most common cancer worldwide, accounting for over 1.37 million deaths annually. The clinical outcome and management of lung cancer patients could be substantially improved by the implementation of non‐invasive biomarker assays for the early detection, prognosis as well as prediction and monitoring of treatment response. MicroRNAs (miRNAs) have been implicated in the regulation of virtually all signaling circuits within a cell and their dysregulation has been shown to play an essential role in the development and progression of cancer. Recently, miRNAs were found to be released into the circulation and to exist there in a remarkably stable form. Furthermore, various cancers were shown to leave specific miRNA fingerprints in the blood of patients suggesting that cell‐free miRNAs could serve as non‐invasive biomarkers for the detection or monitoring of cancer and putative therapeutic targets. Since that, a considerable effort has been devoted to decode the information carried by circulating miRNAs. In the current review, we give an insight into the mechanisms of miRNA release into the bloodstream, their putative functional significance and systematically review the studies focused on the identification of cell‐free miRNAs with the diagnostic, prognostic, and predictive significance in lung cancer and discuss their potential clinical utility. © 2012 Wiley Periodicals, Inc.     

Liver metastatic disease: new concepts and biomarker panels to improve individual outcomes

Liver cancer, one of the leading causes of all cancer related deaths, belongs to the most malignant cancer types. In fact, the secondary hepatic malignancies (liver metastases) are more common than the primary ones. Almost all solid malignancies can metastasise to the liver. It is well justified that the “treat and wait” approach in the overall management of the liver cancer is not up-to-date and so creation of complex individual patient profiles is needed. This review is specifically focused on the liver metastases originating from the colorectum, breast and prostate cancer. Innovative multilevel diagnostics may procure specific panels of validated biomarkers for predisposition, development and progression of metastatic disease. Creation of the patient specific “molecular portrait” is an essential part of the diagnostic strategy. Contextually, analysis of molecular and cellular patterns in blood samples as the minimally invasive diagnostic tool and construction of diagnostic windows based on individual patient profiling is highly recommended for patient cohorts predisposed to and affected by the liver metastatic disease. Summarised information on risk assessment, predictive and prognostic panels for diagnosis and treatments of the liver metastatic disease in colorectal, breast and prostate cancer is provided.     

A field guide for cancer diagnostics using cell‐free DNA: From principles to practice and clinical applications

Recently, many genome‐wide profiling studies provided insights into the molecular make‐up of major cancer types. The deeper understanding of these genetic alterations and their functional consequences led to the discovery of novel therapeutic opportunities improving clinical management of cancer patients. While tissue‐based molecular patient stratification is the gold standard for precision medicine, it has certain limitations: Tissue biopsies are invasive sampling procedures carrying the risk of complications and may not represent the entire tumor due to underlying genetic heterogeneity. In this context, complementary characterization of genetic information in the blood of cancer patients can serve as minimal‐invasive ‘liquid biopsy’. Fragments of circulating cell‐free DNA (cfDNA) are released from tissues of healthy individuals as well as cancer patients. The fraction of cfDNA that is released from primary tumors or metastases (i.e. circulating tumor DNA, ctDNA) represents genetic aberrations in cancer cells, which are a potential source for diagnostic, prognostic, and predictive biomarkers. Recent studies have demonstrated technical feasibility and clinical applications including detection of drug targets and resistance mutations as well as longitudinal monitoring of tumors under therapy. To this end, a variety of pre‐analytical procedures for blood processing, isolation and quantification of cfDNA are being employed and several analytical methods and technologies ranging from PCR‐based single locus assays to genome‐wide approaches are available, which considerably differ in sensitivity, specificity, and throughput. However, broad implementation of ctDNA analysis in daily clinical practice requires a thorough understanding of theoretical, technical, and biological concepts and necessitates standardization and validation of pre‐analytical and analytical procedures across different technologies. Here, we review the pertinent literature and discuss the advantages and limitations of available methodologies and their potential applications in molecular diagnostics.     

Tumor-infiltrating lymphocytes and PD-L1 in breast cancer (and,what happened to medullary carcinoma?)

Tumor-infiltrating lymphocytes (TILs) and PD-L1 have emerged as important immune biomarkers in breast cancer, particularly triple negative breast carcinomas (TNBC) and human epidermal growth factor-2 positive (HER-2⁺) breast carcinomas. These components of the tumor immune microenvironment can be harnessed or targeted with immunotherapy, which represents a significant advancement in the management of TNBC. TILs are a prognostic biomarker in breast cancer, and this recognition has led to reclassification of medullary carcinoma (which were TILs rich by definition) as a pattern of invasive ductal carcinoma (no special type) rather than a distinct histologic type. PD-L1 is a predictive biomarker in TNBC, and two different PD-L1 assays have been approved as companion diagnostics for immune checkpoint inhibition in TNBC. This review will cover the roles of TILs and PD-L1 testing in breast cancer, both of which provide important clinical information to guide patient prognosis and therapy. This is a rapidly evolving and exciting field with significant implications for patient care.     

Dermatopathology in the age of molecular biology

Proctor I, Stoeber K & Williams G H
(2010) Histopathology 57, 1–13
Biomarkers in bladder cancer Cancer biomarkers provide an opportunity to diagnose tumours earlier and with greater accuracy. They can also identify those patients most at risk of disease recurrence and predict which tumours will respond to different therapeutic approaches. Such biomarkers will be especially useful in the diagnosis and management of bladder cancer. At present, bladder tumours are diagnosed and followed‐up using a combination of cystoscopic examination, cytology and histology. These are not only expensive, but also highly subjective investigations and reveal little about the underlying molecular characteristics of the tumour. In recent years numerous diagnostic and prognostic biomarkers of bladder cancer have been identified. Two separate approaches to biomarker discovery have been employed. The first is hypothesis‐driven and focuses upon proteins involved in molecular pathways known to be implicated in tumorigenesis. An alternative approach has been to study the global expression of genes (so‐called ‘genomics’) looking for characteristic signatures associated with disease outcomes. In this review we summarize the current state of biomarker development in this field, and examine why so few have made the successful transition into the clinic. Finally, we introduce a novel approach to biomarker development utilizing components of the DNA replication licensing machinery.     

Bench to bedside: research influencing clinical practice in breast cancer

Based on recent evidence derived from clinical trials and translational research, breast cancer pathology has witnessed a rapid increase in the utilization of predictive markers, companion diagnostics and molecular testing for tailored management of patients with breast cancer. New diagnostic entities with specific molecular phenotypes have also been included in the classification of breast cancer. Genomic assays including Oncotype DX®21-gene Recurrence Score (RS), Prosigna and EndoPredict are currently used in routine practice to guide adjuvant/neoadjuvant therapy. The analysis of established biomarkers such as ER and PR immunohistochemistry has been updated to recognize new categories with different clinical behaviour and significance, such as the ER low expressors and HER2 low carcinomas. PD-L1 testing and PIK3CA mutation have been introduced for advanced TNBC and recurrent ER positive breast cancer respectively. This review provides an update on the rapidly evolving field of predictive & prognostic markers, companion diagnostics, molecular and genomic testing of breast cancer.     

TGF-beta 1 could be a missing link in the interplay between ER and HER-2 in breast cancer

Breast cancer is a very heterogeneous disease considering a number of biomarkers which are under investigation. However, most important biomarkers in a clinical setting are ER (estrogen receptors) and HER-2 (human epidermal growth factor receptor 2), but still only as predictive markers for tamoxifen and trastuzumab therapy. Their prognostic role is still subject of investigation. On the other hand, although, TGF-beta1 is known as marker of invasiveness and metastatic capacity of breast cancer cells, this marker has never been considered to be introduced in routine clinical setting. TGF-beta1 is ER regulated biomarker which act synergistically with HER-2. Aim of this study is to show that clinical significance of determination ER and HER-2 status could be improved, when they are related with TGF-beta1 as additional biomarker. It seems that TGF-beta1 could make a difference regarding prognosis and prediction in breast cancer patients. This hypothesis could be easily verified in corresponding clinical research.     

Exhaled breath condensate as a source of biomarkers for lung carcinomas. A focus on genetic and epigenetic markers—A mini‐review

Lung carcinoma is one of the most common causes of cancer‐related mortality worldwide. It is an aggressive tumor, often diagnosed at an advanced stage when treatment options are limited. Currently, the importance of detection and assessment of various genetic alterations in cancer is recognized as they can serve as very helpful markers in early diagnosis and follow‐up of treatment regimens. Recently, several therapeutically important genetic markers have been identified. One major problem is that tumor tissue specimens used to assay these genetic biomarkers are not always available, especially in the early stages of the disease. Therefore, exhaled breath condensates (EBC) could represent a good non‐invasive source to allow the evaluation of these important genetic markers; these could help in the diagnosis, follow‐up of the disease and/or assessment of treatment efficacy. The key aims of this review are first to describe the origin and constituents of EBC, as well as the different methodological procedures used in studying EBC biomarkers, and second, to document genetic and epigenetic markers that have been analyzed in EBC from lung cancer patients and to estimate their diagnostic and prognostic value. © 2016 Wiley Periodicals, Inc.     

Bench to bedside: research influencing clinical practice in prostate pathology

Prostate cancer is biologically heterogeneous ranging from clinically indolent disease that “old men die with” to aggressive tumours that metastasise and cause death. Optimal management of this disease requires accurate prognostication to avoid over-treatment of the former and prompt appropriate treatment of the latter. Prognostication of prostate cancer is challenging as tumour is often not well visualized on radiological examination, is often detected in non-targeted systematic biopsies and cannot be subjected to a wide local excision for detailed histological examination. Several histopathological parameters that aid risk stratification of prostate cancer have been identified but some tumours lacking adverse pathology findings exhibit aggressive behaviour. Tissue biomarkers could improve the accuracy of prognostication of prostate cancer. This review outlines how histopathological research has impacted the diagnosis, prognostication, and treatment of prostate cancer. We also highlight limitations of the current evidence base and outline the role of the practicing histopathologist in optimizing the clinical utility of biomarker assays.     

ER,PR and HER2 testing in breast cancer

The application of targeted therapies has played important roles in the improvement of breast cancer survival rate during the past two decades. Estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) are well established biomarkers for breast cancer prognosis and for guiding treatment. Emerging data furthers our understanding of the biomarkers and their validity as predictive and prognostic indicators. Breast cancer biomarker testing guidelines have been recently updated. There are still several key challenges in the evaluations of these markers, including pre-analytic standards, tissue selection for testing and re-testing, result interpretations, and tumour heterogeneity. In addition to ER, PR and HER2, newer markers and multigene testings may provide additional information in guiding targeted therapy for breast cancer.     

Biomarkers for gastric cancer: prognostic,predictive or targets of therapy?

Gastric cancer is an aggressive disease often diagnosed at an advanced stage. Despite improvements in surgical and adjuvant treatment approaches, gastric cancer remains a global public health problem with a 5-year overall survival of less than 25 %. This is a heterogeneous disease, both in terms of biology and genetics, and many prognostic biomarkers have been pointed out in the literature; nevertheless, their application remains debatable. In this review, we opted to give relevance to those biomarkers that have been the subject of studies with significant statistical power, which have been replicated and have been/are in targeted therapy clinical trials and, which as a consequence, have their prognostic and/or predictive value established. Some gastric cancer biomarkers that may help in defining the course of treatment are also discussed. Accepted practical guidelines, wet-lab protocols for the detection of these biomarkers, as well as ongoing and completed clinical trials have been compiled. In summary, clinical approaches based on the combination of correct staging with targeted and conventional systemic therapies may improve gastric cancer patients’ outcome, but are only in their infancy. Some major challenges in identifying reliable prognostic/predictive biomarkers are individual genetic variation and tumour heterogeneity that often influence response to therapy and drug resistance. Prognostic and predictive biomarkers may nevertheless be extremely valuable to correctly stratify gastric cancer patients for treatment and, ultimately, improve survival.     

Getting it right: designing microarray (and not 'microawry') comparative genomic hybridization studies for cancer research

The development of high-resolution microarray-based comparative genomic hybridization (aCGH), using cDNA, bacterial artificial chromosome (BAC) and oligonucleotide probes, is providing tremendous opportunities for translational research by facilitating detailed analysis of entire cancer genomes in a single experiment. However, this technology will only fulfil its promise if studies incorporating aCGH are designed with a full understanding of its current limitations and the strategies available to circumvent them. While there have been several excellent reviews on the current status of this technology, there is currently very little guidance available regarding the appropriate design of experiments incorporating aCGH (including the strengths and weaknesses of each platform), and how best to combine the results obtained from aCGH with other 'omic' technologies, including gene expression. In this review, we present the key design issues that need to be considered in order to optimize aCGH studies, including sample selection, the definition of appropriate experimental objectives, arguments for and against the various microarray platforms that are currently available, and methods for data validation and integration. It is envisaged that future well-designed aCGH studies will enhance our understanding of the genetic basis of cancer, and lead to the identification of novel predictive and prognostic cancer biomarkers, as well as molecular therapeutic targets in cancer.     

SELDI ProteinChip(R) Array Technology: Protein-Based Predictive Medicine and Drug Discovery Applications

Predictive medicine, utilizing the ProteinChip^® Array technology, will develop through the implementation of novel biomarkers and multimarker patterns for detecting disease, determining patient prognosis, monitoring drug effects such as efficacy or toxicity, and for defining treatment options. These biomarkers may also serve as novel protein drug candidates or protein drug targets. In addition, the technology can be used for discovering small molecule drugs or for defining their mode of action utilizing protein-based assays. In this review, we describe the following applications of the ProteinChip Array technology: (1) discovery and identification of novel inhibitors of HIV-1 replication, (2) serum and tissue proteome analysis for the discovery and development of novel multimarker clinical assays for prostate, breast, ovarian, and other cancers, and (3) biomarker and drug discovery applications for neurological disorders.     

Prognostic tissue markers in melanoma

Prognostic tissue markers in melanoma Prognosis for patients diagnosed with cutaneous melanoma is currently based upon histopathological features alone, although tumours which are morphologically similar can behave differently. Numerous putative biomarkers have been identified in an attempt to aid prognostication for primary melanoma, using methods which include immunhistochemistry, polymerase chain reaction (PCR), array comparative genomic hybridization (CGH) and gene expression arrays. Despite this wide body of research, no biomarkers for prognosis in melanoma have been translated or are close to translation into clinical practice. In this review selected prognostic biomarkers are evaluated and the factors influencing successful biomarker translation, including phases of biomarker development and study design, are explored in an attempt to highlight the current gap between prognostic melanoma biomarker research and clinical translation.     

Prognostic biomarkers in colorectal cancer: where do we stand?

Colorectal cancer remains a major cause of cancer-related death worldwide. One way to reduce its staggering mortality rate and socio-economic burden is to predict outcome based on the aggressiveness of the tumor biology in order to treat patients accordingly to their risk profile. As such, it comes as no surprise that prognostic biomarker discovery is a hot topic in colorectal cancer research. The last two decades have literally produced tons of new data and an avalanche of potential clinically applicable biomarkers. This review explores and summarizes data concerning the prognostic strength and clinical utility of current and future tissue biomarkers in the diagnosis and treatment of colorectal cancer.