Tissue-based Research Research Articles

Tissue-Based Research in Kidney Cancer: Current Challenges and Future Directions

The past several years have seen unprecedented advances in the application of various therapeutic strategies for the treatment of patients with renal cancer. The availability of active immunotherapy, antiangiogenic therapy, and targeted therapy for this disease has brought front and center issues related to choosing the appropriate treatment for particular patient populations. It is increasingly evident that the most promising treatment selection strategies will incorporate identifying specific features of the tumor itself. To facilitate this move toward personalized medicine, it is critically important to establish some standard principles for renal cancer tissue collection, preparation, and analysis for translational research studies. In this article, we identify and discuss some critical issues related to tissue-based kidney cancer research. We focus on five major areas as follows: (a) surgical and image-guided techniques for tissue collection; (b) quality control of specimen collection, processing, storage, and review; (c) issues related to analysis of paraffin embedded tissues; (d) genomic studies; and (e) assessment of reproducibility of assays across institutions. In addition, some practical implementation strategies are proposed. Although many of the topics discussed are specific for renal cancer, several are also relevant to tissue based biomarker investigations in a broad array of malignancies.

Reliability of Post-Mortem Psychiatric Diagnosis for Neuroscience Research

The validity of post-mortem human brain research relies upon accurate clinical and psychopathological diagnosis. Current literature indicates few instances where standardized diagnostic assessment tools such as the Diagnostic Instrument for Brain Studies have been utilized. The primary aim of the present study was to investigate the degree of concordance between predominant ante-mortem psychiatric diagnoses indicated in medical records, and post-mortem diagnoses derived through structured diagnostic instruments such as the Diagnostic Instrument for Brain Studies and the Item Group Checklist of the Schedules for Clinical Assessment in Neuropsychiatry. Fifty-eight subjects from the New South Wales Tissue Resource Centre, assigned a clinical psychiatric diagnosis after death, were included in the study. The predominant ante-mortem diagnosis of each case was compared to the corresponding post-mortem diagnosis obtained through structured case reviews to which either the Diagnostic Instrument for Brain Studies (from 2001) or the Item Group Checklist of Schedules for Clinical Assessment in Neuropsychiatry (before 2001) were applied. Comparison of ante-mortem and post-mortem diagnoses produced an overall kappa coefficient of 0.66. Kappa coefficients for the schizophrenia cohort were 0.61, 0.35 for the schizoaffective cohort, 0.95 for the major depressive disorder cohort and 0.70 for the bipolar disorder cohort. There was moderate-excellent inter-rater reliability for most cohorts in this sample. There was sufficient disagreement, however, particularly for the schizoaffective cohort, to suggest the value of applying a standardized and structured assessment approach to psychiatric diagnosis. A standardized approach would likely enhance both the accuracy of diagnosis and the prospective validity of tissue-based research. The present study also highlights the importance of accurate and detailed medical record keeping at a symptom-based level across all mental health professions. In the absence of clear and adequate symptom-based detail, the reliability of both ante-mortem and post-mortem diagnosis may be compromised.

Towards a new era of tissue-based diagnosis and research

Molecular investigation of tissue obtained from patients with many chronic illnesses is becoming increasingly important. Using the example of childhood cancer, we show how such investigations contribute in important ways to understanding the underlying pathophysiological basis of disease, determining optimal patient management, and identifying targets for potential new novel therapeutic approaches. Tissue banks are now recognized as an important resource for biomedical research in this area. Challenges for the future of tissue-banking include formalization of technical matters, including the generation of standard operating procedures and quality-control methods. More complex challenges attend the legal and ethical issues in tissue banking. Notwithstanding recent UK legislation, there are many legal uncertainties. Use of excised tissue in research is often claimed to raise a range of ethical issues, but it is not at all clear that public confidence and support for tissue-based research is as negative as some accounts in the socio-anthropological and ethical literature would suggest. Nonetheless, ensuring confidence and trust in tissue-banking will remain an important objective, and the possibilities of novel governance structures should be explored.

Expression Profiling of Melanoma Cell Lines: In Search of A Progression-Related Molecular Signature

Evaluation of: Ryu B, Kim DS, DeLuca AM, Alani RM: Comprehensive expression profiling of tumor cell lines identifies molecular signatures of melanoma progression. PLoS ONE. 2(7), E594 (2007). Using well-established cell lines derived from the various growth phases of cutaneous malignant melanoma, Ryu et al. have succeeded in identifying a molecular signature of melanoma progression. In line with previous studies on human melanoma samples, this signature shows upregulation of genes involved in cell-cycle progression, DNA replication and repair, and resistance to apoptosis, as well as downregulation of genes involved in adhesion and differentiation. In addition, the data point towards an early loss of various tumor suppressor genes and a central role for nuclear factor−κB in melanoma progression. Although this study does not take into account the possible input of the tumor microenvironment in melanoma progression, these data will further stimulate tissue-based research and may add to the development of therapeutic targets in disseminated melanoma.

Motivating Donors to Genetic Research? Anthropological Reasons to Rethink the Role of Informed Consent

In this article we explore the contribution from social anthropology to the medical ethical debates about the use of informed consent in research, based on blood samples and other forms of tissue. The article springs from a project exploring donors' motivation for providing blood and healthcare data for genetic research to be executed by a Swedish start-up genomics company. This article is not confined to empirical findings, however, as we suggest that anthropology provides reason to reassess the theoretical understanding of autonomy as generally defined by Beauchamp and Childress. Careful consideration of the trust expressed by donors through the act of donation, furthermore, suggests that there is reason to redirect the ethical scrutiny from informed consent to issues concerning institutional arrangements and social responsibility. In particular, we suggest that an anthropological approach could facilitate a reconsideration of the political implications of using informed consent as a regulatory practice in tissue-based research.

Informed consent and biobanks: a population-based study of attitudes towards tissue donation for genetic research.

The procurement and usage of tissue samples has begun receiving increasing legal and ethical attention. The authors' aim was to develop an empirically based understanding of public attitudes to the use of tissue for research. A questionnaire was distributed to a randomized sample (n=1,000) of the population in the age group 18-85 in Västerbotten County, Sweden. The response rate was approximately 60%. There was a general acceptance of genetic research based on biobank material (71%) but, though it is often a prerequisite for tissue-based research, a majority (62%) would not allow researchers to examine their healthcare records without specific consent. A majority (66.8%) accepted surrogate decisions by research ethical committees; 48% of the respondents estimated that they would feel respected if they were notified each time a sample was used. When compared and ranked with other issues, informed consent was a principal concern to a minority (4%) only. Should research efforts generate information on future health risks, a majority (55%) would want to be told only if treatment was available. Though genetic research in bioethical debate is often viewed as a potential threat to the integrity of the donor, the confidentiality of medical records still seems to concern donors more. Research ethical committees have support in the majority of the population for some surrogate decisions. The current emphasis on the question of informed consent in policy making for biobank-based research does not seem to be reflected unambiguously in the concerns of the general public.

Constructing Tissue Microarrays for Research Use

Tissue microarrays (TMAs) were recently developed to facilitate tissue-based research. TMAs can be used for any type of study where standard tissue slides have previously been used. However, there are numerous advantages in using TMAs. TMAs allow for screening of a large number of tissue samples under similar experimental conditions. They are also useful in that they conserve tissue and resources and can greatly multiply the number of experiments that can be performed with a limited amount of tissue samples. The basic protocol in this unit discusses how to prepare and cut tissue microarray slides. The resulting arrays may then be constructed manually or automatically, as described in the support protocols.

Advantages and applications of tissue microarray technology on cancer research

To provide evidences for exploiting tissue microarray (TMA) technology, we reviewed advantages and applications of TMA on tumor research. TMA has many advantages, including (1) section from TMA blocks can be utilized for the simultaneous analysis of up to 1,000 different tumors at DNA, RNA or protein level; (2) TMA is highly representative of their donor tissues; (3) TMA can improve conservation of tissue resources and experimental reagents, improve internal experimental control, and increase sample numbers per experiment, and can be used for large-scale, massively parallel in situ analysis; (4) TMA facilitates rapid translation of molecular discoveries to clinical applications. TMA has been applied to tumor research, such as glioma, breast tumor, lung cancer and so on. The development of novel biochip technologies has opened up new possibilities for the high-throughput molecular profiling of human tumors. Novel molecular markers emerging from high-throughput expression surveys could be analyzed on tumor TMA. It is anticipated that TMA, a new member of biochip, will soon become a widely used tool for all types of tissue-based research. TMA will lead to a significant acceleration of the transition of basic research findings into clinical applications.

Web-based tissue microarray image data analysis: Initial validation testing through prostate cancer Gleason grading

Tissue microarray technology promises to enhance tissue-based molecular research by allowing improved conservation of tissue resources and experimental reagents, improved internal experimental control, and increased sample numbers per experiment. Organized, well-validated collection and analysis of the voluminous image data produced by tissue microarray technology is critical to maximize its value. Web-based technology for visual analysis and searchable storage of microarray image data could provide optimal flexibility for research groups in meeting this goal, but this approach has not been examined scientifically. Toward this goal, a prostate tissue microarray block containing 432 tissue cores (0.6 mm diameter) was constructed. Moderately compressed (200 kb).jpg images of each tissue spot were acquired and were saved using a naming convention developed by the SPORE Prostate Tissue Microarray Collaborative Group. Four hundred three tissue array spot images were uploaded into a database developed for this study and were converted to.fpx format to decrease Internet transmission times for high-resolution image data. In phase I of the image analysis portion of the study, testing and preliminary analysis of the Web technology was performed by 2 pathologists (M.A.R. and G.S.B.). In phase II, 2 pathologists (J.I.E. and T.M.W.) with no previous exposure to this technology and no knowledge of the structure of the study were presented a set of 130 sequential tissue spot images via the Web on their office computers. In phase III, the same pathologists were presented a set of 193 images, including all 130 from phase II and 63 others, with image presentation order randomized. With each zoomable tissue spot image, each pathologist was presented with a nested set of questions regarding overall interpretability of the image, presence or absence of cancer, and predominant and second most frequent Gleason grade. In phases II and III of the study, 319 of 323 (99%) image presentations using this Web technology were rated interpretable. Comparing the 2 pathologists' readings in phases II and III, Gleason grade determinations by each pathologist were identical in 179 of 221 (81%) determinations and were within 1 point of each other in 221 of 221 (100%) determinations, a performance rate similar to if not better than that previously reported for direct microscopic Gleason grading. Interobserver comparison of Gleason score determinations and intraobserver comparisons for Gleason grade and score also showed a pattern of uniformity similar to those reported in direct microscope-based Gleason grading studies. Interobserver (7.5%) and intraobserver (5% and 3%) variability in determining whether diagnosable cancer was present point out the existence of a “threshold effect” that has rarely been studied but may provide a basis for identification of features that are most amenable to improved diagnostic standardization. In summary, storage and analysis of tissue microarray spot images using Web-based technology is feasible and practical, and the quality of images obtained using the techniques described here appears adequate for most tissue-based pathology research applications. HUM PATHOL 32:417-427. Copyright © 2001 by W.B. Saunders Company

Tissue microarray (TMA) technology: miniaturized pathology archives for high-throughput in situ studies.

Tissue microarray (TMA) technology allows a massive acceleration of studies correlating molecular in situ findings with clinico-pathological information. In this technique, cylindrical tissue samples are taken from up to 1000 different archival tissue blocks and subsequently placed into one empty 'recipient' paraffin block. Sections from TMA blocks can be used for all different types of in situ tissue analyses including immunohistochemistry and in situ hybridization. Multiple studies have demonstrated that findings obtained on TMAs are highly representative of their donor tissues, despite the small size of the individual specimens (diameter 0.6 mm). It is anticipated that TMAs will soon become a widely used tool for all types of tissue-based research. The availability of TMAs containing highly characterized tissues will enable every researcher to perform studies involving thousands of tumours rapidly. Therefore, TMAs will lead to a significant acceleration of the transition of basic research findings into clinical applications.

Human tissue research in the genomic era of medicine: balancing individual and societal interests.

Advances in DNA sequencing technology and in our understanding of the human genome are ushering in a new era of genomic medicine, one with dramatic potential to not only benefit society through research involving human tissue, but also to cause economic or psychosocial harms to tissue donors and their families. This delicate situation requires that the needs of tissue donors be carefully considered and balanced with those of the medical research community, especially on issues concerning confidentiality, consent, and compensation. We analyzed the tensions between tissue donors and researchers over the research use of human tissue. We also reviewed several approaches, including the establishment of tissue-trustee infrastructures at academic medical centers, aimed at achieving a more equitable balance between individual donor protection and societal benefits derived from tissue-based research. Arch Intern Med. 2000;160:3377-3384.

The role of the pathologist as tissue refiner and data miner: the impact of functional genomics on the modern pathology laboratory and the critical roles of pathology informatics and bioinformatics.

This article provides an overview of how functional genomics is likely to impact on the pathology laboratory and highlights how informatics and tissue banking will greatly facilitate the molecular age of medicine. Important aspects of functional genomics in the post-genome era, including the roles of laser capture microdissection, DNA- and complementary DNA-based microarrays, proteomic methods, collaborative human tissue banking, tissue microarrays, and pathobioinformatics in the modern pathology laboratory are discussed. The role of mass spectroscopy in the analysis of RNA, DNA, and protein and its impact on the clinical laboratory, particularly in cost-effectiveness and time savings, are evaluated. This article explores how laboratory information systems (LISs) and the devices that feed them information may need to be modified to adapt to greater volumes of data for the new testing modalities that require understanding sophisticated fluorescence detection methods and image processing. Emerging genomic testing methods and their impact on pathology laboratory testing, especially in the area of molecular classification of neoplasms, are examined. The role of the tissue bank in the modern pathology laboratory as an archive of control normal tissues, as well as subsamples of the spectrum of progressive neoplastic states, is discussed in light of its critical importance to the molecular classification of cancer. Establishing a database that combines structured reports in pathology LISs and construction of tissue banking information systems will provide a rich resource for pathology departments. The article discusses a hypothetical resource, such as the Shared Tumor Expression Profiler, that would provide access to well-characterized tissue-based research resources for clinicians and researchers. Last, the article emphasizes how LISs can prepare for these changes, and how training pathologists in pathology informatics and bioinformatics (pathobioinformatics) is critical to ensure pathology's overall leadership role in the post-genome era.