Issues in collecting, processing and storing human tissues and associated information to support biomedical research

Assessment of formalin preserved and fresh frozen quadriceps tendon graft-suture constructs for load to failure testing: a biomechanical cadaveric study

PURPOSE

Fresh-frozen specimen availability and cost may be a barrier for initiation of biomechanical studies where soft tissue is used in a construct with other medical devices. The impact of soft tissue preservation method on the outcomes of biomechanical studies in the specific case of graft-suture constructs is relatively unexplored. This study aimed to observe peak loads and failure modes in biomechanical testing of fresh-frozen (FF) versus formalin embalmed (FE) quadriceps tendon (QT) graft-suture constructs for soft tissue fixation in ACLR and assess suitability of FE QT graft constructs for load-to-fail testing.

METHODS

Twenty QT grafts were harvested from human cadaver specimens. Ten grafts came from fresh-frozen donors and 10 from embalmed donors. All grafts were prepared with the modified Prusik knot using a braided composite suture and subjected to tensile loading. Comparisons between the biomechanical properties of the graft-suture constructs were made with unpaired t tests with α = 0.05.

RESULTS

FE and FF constructs displayed similar peak loads and failure modes. FF constructs had greater elongation after pre-tensioning than FE (7.3 vs. 5.5 mm, p = 0.02) and greater elongation after cyclic loading than FE constructs (17.5 vs. 10.5 mm, p = 0.01). Hysteresis was greater for FF constructs at the 50th, 100th, 150th, and 200th cycle (p = 0.02, p = 0.07, p < 0.001, p = 0.004, respectively). FE constructs were stiffer than fresh-frozen (103 vs. 84 N/mm, p < 0.001).

CONCLUSION

FE constructs were significantly stiffer but displayed similar peak load and failure mode to FF which was reflective of the strength of the suture material. FE grafts can offer an alternative to FF grafts in graft-suture constructs for biomechanical studies where load at failure and knot security and strength is of main interest.

Techniques, procedures, and applications in host genetic analysis

This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.

Systems Biology Approach to Analyze Microarray Datasets for Identification of Disease-Causing Genes: Case Study of Oral Squamous Cell Carcinoma

The discovery of potential disease-causing genes can aid medical progress. The post-genomic era has made this a more difficult task. Modern high-throughput methods have not solved the problem of identifying disease genes. Conventional methods cannot be used to investigate many rare or lethal diseases. Monitoring gene expression values in different samples using microarray technology is one of the best and most accurate ways to identify disease-causing genes. One of the most recent advances in experimental molecular biology is microarrays, which allow researchers to simultaneously monitor the expression levels of thousands of genes. Statistical analysis of microarray data might aid gene discovery by revealing pathways related to the target gene and facilitating identification of candidate genes. Systems biology, an interdisciplinary approach, has emerged as a crucial analytic tool with the potential to reveal previously unidentified causes and consequences of human illness. Genetic, environmental, immunological, or neurological factors have been implicated in the developing complex disorders like cancer. Because of this, it is important to approach the study of such disease from a novel perspective. The system biology approach allows us to rapidly identify disease-causing genes and assess their viability as therapeutic targets. This chapter demonstrates systems biology approaches to identify candidate genes using public database. Oral squamous cell carcinoma (OSCC) is used as a model disease to show how systems biology can be used successfully to identify and prioritize disease genes.

The Cooperative Human Tissue Network of the National Cancer Institute: Supporting Cancer Research for 35 Years

The Cooperative Human Tissue Network was created by the NCI in 1987 to support a coordinated national effort to collect and distribute high quality, pathologist-validated human tissues for cancer research. Since then, the network has expanded to provide different types of tissue samples, blood and body fluid samples, immunohistologic and molecular sample preparations, tissue microarrays, and clinical datasets inclusive of biomarkers and molecular testing. From inception through the end of 2021, the network has distributed 1,375,041 biospecimens. It served 889 active investigators in 2021. The network has also taken steps to begin to optimize the representation of diverse communities among the distributed biospecimens. In this article, the authors review the 35-year history of this network, describe changes to the program over the last 15 years, and provide operational and scientific highlights from each of the divisions. Readers will learn how to engage with the network and about the continued evolution of the program for the future.

A cadaveric breast cancer tissue phantom for phase-contrast X-ray imaging applications

BACKGROUND

As mammography X-ray imaging technologies advance and provide elevated contrast in soft tissues, a need has developed for reliable imaging phantoms for use in system design and component calibration. In advanced imaging modalities such as refraction-based methods, it is critical that developed phantoms capture the biological details seen in clinical precancerous and cancerous cases while minimizing artifacts that may be caused due to phantom production. This work presents the fabrication of a breast tissue imaging phantom from cadaveric breast tissue suitable for use in both transmission and refraction-enhanced imaging systems.

METHODS

Human cancer cell tumors were grown orthotopically in nude athymic mice and implanted into the fixed tissue while maintaining the native tumor/adipose tissue interface.

RESULTS

The resulting human-murine tissue hybrid phantom was mounted on a clear acrylic housing for absorption and refraction X-ray imaging. Digital breast tomosynthesis was also performed.

CONCLUSION

Both attenuation-based imaging and refraction-based imaging of the phantom are presented to confirm the suitability of this phantom's use in both imaging modalities.

The Use of Human Tissues for Research: What Investigators Need to Know

While laboratory animals are necessary for some aspects of the development of scientific and biomedical advances, including those of precision medicine, the use of human tissues is necessary in order to explore the findings and ensure that they are relevant to human systems. Many sources of human tissues exist, but researchers - particularly those making the transition from animal to human systems - may not be aware of how best to find quality sources of human tissues or how best to use them in their research. In this article, we discuss the advantages of using human tissues in research. In addition, we highlight some of the major advances made possible through the use of human tissue, and describe how human tissue is collected for research. We discuss the various types of bioresources that make human tissue available, and advise on how investigators can find and use appropriate bioresources to support their research - with the hope that this information will help facilitate the transition from research on animals to research using human tissues, as rapidly as is practicable.

The Availability of Human Biospecimens to Support Biomarker Research

Preserved biospecimens held in biobank inventories and clinical archives are important resources for biomarker research. Recent advances in technologies have led to an increase in use of clinical archives in particular, in order to study retrospective cohorts and to generate data relevant to tissue biomarkers. This raises the question of whether the current sizes of biobank inventories are appropriate to meet the demands of biomarker research. This commentary discusses this question by considering data concerning overall biobank and biospecimen numbers to estimate current biospecimen supply and use. The data suggests that biospecimen supply exceeds current demand. Therefore, it may be important for individual biobanks to reassess the targets for their inventories, consider culling unused portions of these inventories, and shift resources towards providing prospective custom biobanking services.

Systems Biology Approaches to Decipher the Underlying Molecular Mechanisms of Glioblastoma Multiforme

Glioblastoma multiforme (GBM) is one of the most malignant central nervous system tumors, showing a poor prognosis and low survival rate. Therefore, deciphering the underlying molecular mechanisms involved in the progression of the GBM and identifying the key driver genes responsible for the disease progression is crucial for discovering potential diagnostic markers and therapeutic targets. In this context, access to various biological data, development of new methodologies, and generation of biological networks for the integration of multi-omics data are necessary for gaining insights into the appearance and progression of GBM. Systems biology approaches have become indispensable in analyzing heterogeneous high-throughput omics data, extracting essential information, and generating new hypotheses from biomedical data. This review provides current knowledge regarding GBM and discusses the multi-omics data and recent systems analysis in GBM to identify key biological functions and genes. This knowledge can be used to develop efficient diagnostic and treatment strategies and can also be used to achieve personalized medicine for GBM.

Analysis of Trends in Biospecimen Complexity in Cancer Research Over Two Decades

Background: Over time, researchers' demand for increased quality and quantity of biospecimens has risen. However, quality is multifaceted, ranging from simple to complex, and comes at a cost. Therefore, to be sustainable and ensure optimal utilization of their resources (supply), biobanks must consider the trends in biospecimen use to predict the needs for future biospecimen quality (demand). Methods: An unbiased selection process was used to identify research articles from across the spectrum of cancer research from the PubMed database. A set of 225 articles utilizing human biospecimens were randomly selected for review (75 articles from each of three time intervals; 2000, 2010, 2020). Criteria for determining the source and complexity of quality of biospecimens were developed and overall concordance between two independent observers abstracting the data was then confirmed (k = 0.87) to validate the criteria. Results: We observed increased use of dual biospecimen formats (20%-36% of articles, p = 0.03), matched samples (16%-37% of articles, p = 0.0033), and biospecimens with associated outcomes data (20%-49%, p = 0.0002). In addition, the use of two or more cohorts increased over time (p = 0.03). The mechanism through which biospecimens were obtained also changed over time with an increase in the diversity of collection pathways used (p = 0.006). Conclusions: The complexity of biospecimens being used in cancer research and the diversity of collection pathways through which these are obtained has changed significantly. This observation is important for biobanks given that the cost to support the supply of biospecimens with complex extrinsic as opposed to simple intrinsic quality characteristics is greater. For biobanks to manage sustainability, optimize utilization, and meet changing research demand, they may need to adjust their operational models to better support the supply of these types of biospecimens.

Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel

Biomarker discovery would be an important tool in advancing and utilizing the concept of precision and personalized medicine in the clinic. Discovery of novel variants in local population provides confident targets for developing biomarkers for personalized medicine. We identified the need to generate high-quality sequencing data from local colorectal cancer patients and understand the pattern of occurrence of variants. In this report, we used archived samples from Saudi Arabia and used the AmpliSeq comprehensive cancer panel to identify novel somatic variants. We report a comprehensive analysis of next-generation sequencing results with a coverage of >300X. We identified 466 novel variants which were previously unreported in COSMIC and ICGC databases. We analyzed the genes associated with these variants in terms of their frequency of occurrence, probable pathogenicity, and clinicopathological features. Among pathogenic somatic variants, 174 were identified for the first time in the large intestine. APC, RET, and EGFR genes were most frequently mutated. A higher number of variants were identified in the left colon. Occurrence of variants in ERBB2 was significantly correlated with those of EGFR and ATR genes. Network analyses of the identified genes provide functional perspective of the identified genes and suggest affected pathways and probable biomarker candidates. This report lays the ground work for biomarker discovery and identification of driver gene mutations in local population.

The Human Explanted Heart Program: A translational bridge for cardiovascular medicine

The progression of cardiovascular research is often impeded by the lack of reliable disease models that fully recapitulate the pathogenesis in humans. These limitations apply to both in vitro models such as cell-based cultures and in vivo animal models which invariably are limited to simulate the complexity of cardiovascular disease in humans. Implementing human heart tissue in cardiovascular research complements our research strategy using preclinical models. We established the Human Explanted Heart Program (HELP) which integrates clinical, tissue and molecular phenotyping thereby providing a comprehensive evaluation into human heart disease. Our collection and storage of biospecimens allow them to retain key pathogenic findings while providing novel insights into human heart failure. The use of human non-failing control explanted hearts provides a valuable comparison group for the diseased explanted hearts. Using HELP we have been able to create a tissue repository which have been used for genetic, molecular, cellular, and histological studies. This review describes the process of collection and use of explanted human heart specimens encompassing a spectrum of pediatric and adult heart diseases, while highlighting the role of these invaluable specimens in translational research. Furthermore, we highlight the efficient procurement and bio-preservation approaches ensuring analytical quality of heart specimens acquired in the context of heart donation and transplantation.

Amygdala levels of the GluA1 subunit of glutamate receptors and its phosphorylation state at serine 845 in the anterior hippocampus are biomarkers of ictal fear but not anxiety

Fear is a conscious state caused by exposure to real or imagined threats that trigger stress responses that affect the body and brain, particularly limbic structures. A sub-group of patients with mesial temporal lobe epilepsy related to hippocampus sclerosis (MTLE-HS) have seizures with fear, which is called ictal fear (IF), due to epileptic activity within the brain defensive survival circuit structures. Synaptic transmission efficacy can be bi-directionally modified through potentiation (long-term potentiation (LTP)) or depression (long-term depression (LTD)) as well as the phosphorylation state of Ser831 and Ser845 sites at the GluA1 subunit of the glutamate AMPA receptors, which has been characterized as a critical event for this synaptic plasticity. In this study, GluA1 levels and the phosphorylation at Ser845 and Ser831 in the amygdala (AMY), anterior hippocampus (aHIP) and middle gyrus of temporal neocortex (CX) were determined with western blots and compared between MTLE-HS patients who were showing (n = 06) or not showing (n = 25) IF. Patients with IF had an 11% decrease of AMY levels of the GluA1 subunit (p = 0.05) and a 21.5% decrease of aHIP levels of P-GluA1-Ser845 (p = 0.009) compared to patients not showing IF. The observed associations were not related to imbalances in the distribution of other concomitant types of aura, demographic, clinical or neurosurgical variables. The lower levels of P-GluA1-Ser845 in the aHIP of patients with IF were not related to changes in the levels of the serine/threonine-protein phosphatase PP1-alpha catalytic subunit or protein kinase A activation. Taken together, the GluA1 subunit levels in AMY and P-GluA1-Ser845 levels in the aHIP show an overall accuracy of 89.3% (specificity 95.5% and sensitivity 66.7%) to predict the presence of IF. AMY levels of the GluA1 subunit and aHIP levels of P-GluA1-Ser845 were not associated with the psychiatric diagnosis and symptoms of patients. Taken together with previous findings in MTLE-HS patients with IF who were evaluated by stereotactic implanted depth electrodes, we speculate our findings are consistent with the hypothesis that AMY is not a centre of fear but together with other sub-cortical and cortical structures integrates the defensive circuit that detect and respond to threats. This is the first report to address neuroplasticity features in human limbic structures connected to the defensive survival circuits, which has implications for the comprehension of highly prevalent psychiatric disorders and symptoms.

Sequence-Based Characterization of Intratumoral Bacteria-A Guide to Best Practice

Tumors are hospitable environments to bacteria and several recent studies on cancer patient samples have introduced the concept of an endogenous tumor microbiome. For a variety of reasons, this putative tumor microbiome is particularly challenging to investigate, and a failure to account for the various potential pitfalls will result in erroneous results and claims. Before this potentially extremely medically-significant habitat can be accurately characterized, a clear understanding of all potential confounding factors is required, and a best-practice approach should be developed and adopted. This review summarizes all of the potential issues confounding accurate bacterial DNA sequence analysis of the putative tumor microbiome, and offers solutions based on related research with the hope of assisting in the progression of research in this field.

Metabolomic studies of breast cancer in murine models: A review

BACKGROUND

Metabolomic strategies have been extensively used to search for biomarkers of disease, including cancer, in biological complex mixtures such as cells, tissues and biofluids. In breast cancer research, murine models are of great value and metabolomics has been increasingly applied to characterize tumor or organ tissues, or biofluids, for instance to follow-up metabolism during cancer progression or response to specific therapies.

SCOPE OF REVIEW

This review briefly introduces the different murine models used in breast cancer research and proceeds to present the metabolomic studies reported so far to describe the deviant metabolic behavior associated to breast cancer, in each type of model: xenografts (cell- or patient-derived), spontaneous (naturally-occurring or genetically engineered) and carcinogen-induced. The type of sample and strategies followed are identified, as well as the main findings from of study.

MAJOR CONCLUSIONS

Metabolomics has gradually become relevant in characterizing murine models of breast cancer, using either Nuclear Magnetic Resonance (NMR) or Mass Spectromety (MS). Both tissue and biofluids are matrixes of interest in this context, although in some type of models, reports have focused primarily on the former. The aims of tissue studies have comprised the search for mechanistic knowledge of carcinogenesis, metastasis development and response/resistance to therapies. Biofluid metabolomics has mainly aimed at finding non-invasive biomarkers for early breast cancer detection or prognosis determination.

GENERAL SIGNIFICANCE

Metabolomics provides exquisite detail on murine tumor and systemic metabolism of breast cancer. This knowledge paves the way for the discovery of new biomarkers, potentially translatable to in vivo non-invasive patient follow-up.

The Utilization of Biospecimens: Impact of the Choice of Biobanking Model

The term research "biobank" is one of multiple names (e.g., bioresource, biorepository,) used to designate an entity that receives, collects, processes, stores, and/or distributes biospecimens or other biospecimen-related products (e.g., data) to support research. There are multiple organizational models of biobanking used by bioresources, but the primary goal of all bioresources should not be simply to collect biospecimens, but ultimately to distribute almost all collected biospecimens and/or data to support scientific research; bioresources should serve as "biodistributors" rather than "biovaults." The appropriate choice of model is the first step in ensuring optimal biospecimen utilization by a bioresource. This article discusses some of the different models that may be used alone or in combination by a bioresource providing biospecimens for research; it describes the factors affecting the choice of the most appropriate model or models, the advantages and disadvantages of the various models, and a discussion of the impact of the choice of the model on biospecimen utilization. Frequently, problems with biospecimen utilization are not caused by any single model, but rather a mismatch between the choice of model and goals of the bioresource, and/or problems with the subsequent design, goals, operations, and management of the bioresource after a model is selected.

Influence of Cell Type and Culture Medium on Determining Cancer Selectivity of Cold Atmospheric Plasma Treatment

Increasing the selectivity of cancer treatments is attractive, as it has the potential to reduce side-effects of therapy. Cold atmospheric plasma (CAP) is a novel cancer treatment that disrupts the intracellular oxidative balance. Several reports claim CAP treatment to be selective, but retrospective analysis of these studies revealed discrepancies in several biological factors and culturing methods. Before CAP can be conclusively stated as a selective cancer treatment, the importance of these factors must be investigated. In this study, we evaluated the influence of the cell type, cancer type, and cell culture medium on direct and indirect CAP treatment. Comparison of cancerous cells with their non-cancerous counterparts was performed under standardized conditions to determine selectivity of treatment. Analysis of seven human cell lines (cancerous: A549, U87, A375, and Malme-3M; non-cancerous: BEAS-2B, HA, and HEMa) and five different cell culture media (DMEM, RPMI1640, AM, BEGM, and DCBM) revealed that the tested parameters strongly influence indirect CAP treatment, while direct treatment was less affected. Taken together, the results of our study demonstrate that cell type, cancer type, and culturing medium must be taken into account before selectivity of CAP treatment can be claimed and overlooking these parameters can easily result in inaccurate conclusions of selectivity.

Patient Registries in Idiopathic Pulmonary Fibrosis

Over the past decade, several large registries of patients with idiopathic pulmonary fibrosis (IPF) have been established. These registries are collecting a wealth of longitudinal data on thousands of patients with this rare disease. The data collected in these registries will be complementary to data collected in clinical trials because the patient populations studied in registries have a broader spectrum of disease severity and comorbidities and can be followed for a longer period of time. Maintaining the quality and completeness of registry databases presents administrative and resourcing challenges, but it is important to ensuring the robustness of the analyses. Data from patient registries have already helped improve understanding of the clinical characteristics of patients with IPF, the impact that the disease has on their quality of life and survival, and current practices in diagnosis and management. In the future, analyses of biospecimens linked to detailed patient profiles will provide the opportunity to identify biomarkers linked to disease progression, facilitating the development of precision medicine approaches for prognosis and therapy in patients with IPF.

Commentary on Improving Biospecimen Utilization by Classic Biobanks: Identifying Past and Minimizing Future Mistakes

Many classic biobanks collect more human tissues than they distribute, leading to increased inventories, unnecessary storage, increased expenses, and reduced chargeback income. This situation is a result of biobanks operating without well-defined goals, having incorrect views of the potential number of investigators who will utilize specimens, and collection of biospecimens without adequately considering the need for specific tissues by investigators. These deficiencies frequently lead to unrealistic plans for biospecimen utilization and biobanks that are larger than necessary. For example, tissue collections usually are not periodically compared with biospecimen distribution and modified accordingly. An ethical issue has arisen as to the acceptability of consenting patients for the use of their tissues in research without a realistic planned approach to distribution of the biospecimens and their ultimate utilization in supporting biomedical research. These issues and how to minimize them are discussed in this commentary focused on how classic biobanks can improve utilization of their biospecimens.

Clinical and research applications of a brain tumor tissue bank in the age of precision medicine

Marked progress has been made recently in the treatment of patients with central nervous system (CNS) tumors, especially gliomas. However, because of the relative rarity of these tumors compared with other malignancies, advances in the molecular/genetic analysis leading to future targeted treatments rely on systematic, organized tissue banking. Several large multi-institutional efforts have utilized major tissue banks that have yielded valuable information that may lead to a better understanding of the pathogenesis of CNS tumors. This manuscript portrays best practices for the establishment and maintenance of a well-organized CNS tumor bank. In addition, annotation for clinical and research needs is explained. The potential benefits to clinical care, as well as basic science and translational research are also described.

Computational Analysis of High-Dimensional Mass Cytometry Data from Clinical Tissue Samples

The advent of mass cytometry has resulted in the generation of high-dimensional, single-cell expression data sets from clinical samples. These data sets cannot be effectively analyzed using traditional approaches. Instead, new approaches using dimensionality reduction and network analysis techniques have been implemented to assess these data. Here, detailed methods are described for analyzing immune cell expression from clinical samples using network analyses. Specifically, details are given for performing SCAFFoLD and CITRUS analyses. The methods described will use immune cell tumor infiltrate as an example.

Issues in the Use of Human Tissues to Support Precision Medicine

Precision medicine is an approach in which the characteristics of patients as well as their diseases are used to identify optimal therapy; it links researchers, patients, health care providers, and clinical laboratories. In precision medicine, specific molecular characteristics of an untreatable cancer can be targeted by specific molecular-based therapy. Access to high-quality human tissues is necessary to determine many characteristics of patients and their diseases (such as targetable molecules). There are ethical issues in using human tissues in precision medicine, including informed consent and confidentiality, optimal utilization, quality of tissues, and minimization of bias. When human tissues are obtained for patient therapy, the bioresource should be a component certified by Clinical Laboratory Improvement Amendments. For precision medicine to benefit medically underserved populations requires extensive focused research, planning, and resources, some of which are currently unavailable at rural and other sites where care is provided to underserved populations.

Lessons Learned During Three Decades of Operations of Two Prospective Bioresources

Prospective collection is a model through which biospecimens are provided for research. Using this model, biospecimens are collected based on real-time requests from the research community instead of being collected based on the prediction of future requests. We describe the lessons learned by two bioresources that have operated successfully using a prospective model for over three decades. Our goal is to improve other bioresources by increasing utilization of biospecimens that honor consented donors who provide biospecimens to the research community; this provides strong evidence of stewardship of the public trust. The operation of these sites requires flexibility, close communication, and cooperation with the investigator in developing a standard operating procedure (protocol) based on the investigator's needs described in their initial request. If practicable, almost any preparation can be provided, including fresh (nonfrozen) biospecimens and tissue blots. A quality management system includes rigorous quality control of the specific biospecimens provided to an investigator. The informatics approach focuses on the investigator, the investigator's request, and the biospecimens collected for the investigator; the informatics focus of classic biobanks is on the biospecimens collected to match expected future requests. These lessons have been incorporated into our current operations. Standard investigator agreements (e.g., indemnification and no unapproved biospecimen transfers to third parties) replace material transfer agreements. We have operated under the prospective model of the Cooperative Human Tissue Network (CHTN), which has been successful and has provided over 1.2 million biospecimens since it began in 1987. These tissues have supported over 4300 peer-reviewed scientific articles. Since 2012, about 1000 publications have indicated support by CHTN tissues; their average citation rate is 31 with an H factor of 61. Also, during this period, 114 patents cited the CHTN. We also describe disadvantages of prospective bioresources (e.g., inadequate distribution of rare tissues, biospecimens not immediately available, and delayed clinical outcomes).

Factors that drive the increasing use of FFPE tissue in basic and translational cancer research

The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.

The mechanical properties of fresh versus fresh/frozen and preserved (Thiel and Formalin) long head of biceps tendons: A cadaveric investigation

Human cadaveric specimens commonly serve as mechanical models and as biological tissue donors in basic biomechanical research. Although these models are used to explain both in vitro and in vivo behavior, the question still remains whether the specimens employed reflect the normal in vivo situation. The mechanical properties of fresh-frozen or preserved cadavers may differ, and whether they can be used to reliably investigate pathology could be debated. The purpose of this study was to therefore examine the mechanical properties of cadaveric long biceps tendons, comparing fresh (n=7) with fresh-frozen (n=8), formalin embalmed (n=15), and Thiel-preserved (n=6) specimens using a Universal Testing Machine. The modulus of elasticity and the ultimate tensile strength to failure was recorded. Tensile failure occurred at an average of 12N/mm² in the fresh group, increasing to 40.1N/mm² in the fresh-frozen group, 50.3N/mm² in the formalin group, and 52N/mm² in the Thiel group. The modulus of elasticity/stiffness of the tendon increased from fresh (25.6MPa), to fresh-frozen (55.3MPa), to Thiel (82.5MPa), with the stiffest being formalin (510.6MPa). Thiel-preserved and formalin-embalmed long head of biceps tendons and fresh-frozen tendons have a similar load to failure. Either the Thiel or formalin preserved tendon could therefore be considered as alternatives for load to failure studies. However, the Young's modulus of embalmed tendons were significantly stiffer than fresh or fresh frozen specimens, and these methods might be less suitable alternatives when viscoelastic properties are being investigated.

Powering ex vivo tissue models in microfluidic systems

This Frontiers review analyzes the rapidly growing microfluidic strategies that have been employed in attempts to create physio relevant 'organ-on-chip' models using primary tissue removed from a body (human or animal). Tissue harvested immediately from an organism, and cultured under artificial conditions is referred to as ex vivo tissue. The use of primary (organotypic) tissue offers unique benefits over traditional cell culture experiments, and microfluidic technology can be used to further exploit these advantages. Defining the utility of particular models, determining necessary constituents for acceptable modeling of in vivo physiology, and describing the role of microfluidic systems in tissue modeling processes is paramount to the future of organotypic models ex vivo. Virtually all tissues within the body are characterized by a large diversity of cellular composition, morphology, and blood supply (e.g., nutrient needs including oxygen). Microfluidic technology can provide a means to help maintain tissue in more physiologically relevant environments, for tissue relevant time-frames (e.g., matching the natural rates of cell turnover), and at in vivo oxygen tensions that can be controlled within modern microfluidic culture systems. Models for ex vivo tissues continue to emerge and grow in efficacy as mimics of in vivo physiology. This review addresses developments in microfluidic devices for the study of tissues ex vivo that can serve as an important bridge to translational value.

Cancer oriented biobanks: A comprehensive review

Biobanks provide a platform for innovative biomedical research and has improvised translational and personalized medicine to a great extent. Time 2009 published 10 ideas changing the world right now with biobanks on the list emphasizing its role in discovery and development of new therapeutic drugs. They form the cornerstone, providing resources for future investigations and biomarker discovery to understand the effects of genetic, environmental and lifestyle factors on human morbidity, mortality and health. The aim of this review paper is to understand the role of biobanking in cancer research, the challenges faced and strategies to overcome these, for long term and sustainable research in the field of oncology.

Zebrafish as a model to study bone maturation: Nanoscale structural and mechanical characterization of age-related changes in the zebrafish vertebral column

Zebrafish (Danio rerio) is a useful model for understanding biomedical properties of bone and are widely employed in developmental and genetics studies. Here, we have studied the development of zebrafish vertebral bone at the nanoscale from adolescence (6 months), early adulthood (10 months) to mid-life (14 months). Characterization of the bone was conducted using energy-dispersive X-ray spectroscopy (EDX), scanning electron microscopy (SEM) and PeakForce QNM atomic force microscopy (AFM) techniques. SEM and AFM revealed a lamellar structure with mineralized collagen fibrils. There was a significant increase in the wall thickness from 6 to 10 months (76%) and 10 months to 14 months (26%), which is positively correlated with nanomechanical behavior. An increase in the Ca/P ratio was found which was also positively correlated with nanomechanical properties. The change in mechanical properties and Ca/P are similar to those expected in humans when transitioning from adolescence to mid-life. We suggest that zebrafish serve as a suitable model for further studies on age-related changes in bone ultrastructure.

Human tissue models in cancer research: looking beyond the mouse

Mouse models, including patient-derived xenograft mice, are widely used to address questions in cancer research. However, there are documented flaws in these models that can result in the misrepresentation of human tumour biology and limit the suitability of the model for translational research. A coordinated effort to promote the more widespread development and use of ‘non-animal human tissue’ models could provide a clinically relevant platform for many cancer studies, maximising the opportunities presented by human tissue resources such as biobanks. A number of key factors limit the wide adoption of non-animal human tissue models in cancer research, including deficiencies in the infrastructure and the technical tools required to collect, transport, store and maintain human tissue for lab use. Another obstacle is the long-standing cultural reliance on animal models, which can make researchers resistant to change, often because of concerns about historical data compatibility and losing ground in a competitive environment while new approaches are embedded in lab practice. There are a wide range of initiatives that aim to address these issues by facilitating data sharing and promoting collaborations between organisations and researchers who work with human tissue. The importance of coordinating biobanks and introducing quality standards is gaining momentum. There is an exciting opportunity to transform cancer drug discovery by optimising the use of human tissue and reducing the reliance on potentially less predictive animal models.

Summary: Samuel Jackson and Gareth Thomas discuss the limitations of patient-derived xenograft mouse models and highlight initiatives to maximise the use of human tissue in cancer research, with the goal of improving translation and reducing animal experimentation.

Droplet-based digital PCR and next generation sequencing for monitoring circulating tumor DNA: a cancer diagnostic perspective

INTRODUCTION

Early detection of cancers through the analysis of ctDNA could have a significant impact on morbidity and mortality of cancer patients. However, using ctDNA for early cancer diagnosis is challenging partly due to the low amount of tumor DNA released in the circulation and its dilution within DNA originating from non-tumor cells. Development of new technologies such as droplet-based digital PCR (ddPCR) or optimized next generation sequencing (NGS) has greatly improved the sensitivity, specificity and precision for the detection of rare sequences. Areas covered: This paper will focus on the potential application of ddPCR and optimized NGS to detect ctDNA for detection of cancer recurrence and minimal residual disease as well as early diagnosis of cancer patients. Expert commentary: Compared to tumor tissue biopsies, blood-based ctDNA analyses are minimally invasive and accessible for regular follow-up of cancer patients. They are also described as a better picture of patients' pathology allowing to highlight both tumor heterogeneity and multiple tumor sites. After a brief introduction on the application of the follow-up of ctDNA using genetic or epigenetic biomarkers for prognosis and surveillance of cancer patients, potential perspectives of using ctDNA for early diagnosis of cancers will be presented.

Mechanical characterization of human brain tumors from patients and comparison to potential surgical phantoms

While mechanical properties of the brain have been investigated thoroughly, the mechanical properties of human brain tumors rarely have been directly quantified due to the complexities of acquiring human tissue. Quantifying the mechanical properties of brain tumors is a necessary prerequisite, though, to identify appropriate materials for surgical tool testing and to define target parameters for cell biology and tissue engineering applications. Since characterization methods vary widely for soft biological and synthetic materials, here, we have developed a characterization method compatible with abnormally shaped human brain tumors, mouse tumors, animal tissue and common hydrogels, which enables direct comparison among samples. Samples were tested using a custom-built millimeter-scale indenter, and resulting force-displacement data is analyzed to quantify the steady-state modulus of each sample. We have directly quantified the quasi-static mechanical properties of human brain tumors with effective moduli ranging from 0.17–16.06 kPa for various pathologies. Of the readily available and inexpensive animal tissues tested, chicken liver (steady-state modulus 0.44 ± 0.13 kPa) has similar mechanical properties to normal human brain tissue while chicken crassus gizzard muscle (steady-state modulus 3.00 ± 0.65 kPa) has similar mechanical properties to human brain tumors. Other materials frequently used to mimic brain tissue in mechanical tests, like ballistic gel and chicken breast, were found to be significantly stiffer than both normal and diseased brain tissue. We have directly compared quasi-static properties of brain tissue, brain tumors, and common mechanical surrogates, though additional tests would be required to determine more complex constitutive models.

Effect of cryopreservation on delineation of immune cell subpopulations in tumor specimens as determinated by multiparametric single cell mass cytometry analysis

Background

Comprehensive understanding of cellular immune subsets involved in regulation of tumor progression is central to the development of cancer immunotherapies. Single cell immunophenotyping has historically been accomplished by flow cytometry (FC) analysis, enabling the analysis of up to 18 markers. Recent advancements in mass cytometry (MC) have facilitated detection of over 50 markers, utilizing high resolving power of mass spectrometry (MS). This study examined an analytical and operational feasibility of MC for an in-depth immunophenotyping analysis of the tumor microenvironment, using the commercial CyTOF™ instrument, and further interrogated challenges in managing the integrity of tumor specimens.

Results

Initial longitudinal studies with frozen peripheral blood mononuclear cells (PBMCs) showed minimal MC inter-assay variability over nine independent runs. In addition, detection of common leukocyte lineage markers using MC and FC detection confirmed that these methodologies are comparable in cell subset identification. An advanced multiparametric MC analysis of 39 total markers enabled a comprehensive evaluation of cell surface marker expression in fresh and cryopreserved tumor samples. This comparative analysis revealed significant reduction of expression levels of multiple markers upon cryopreservation. Most notably myeloid derived suppressor cells (MDSC), defined by co-expression of CD66b⁺ and CD15⁺, HLA-DR^dim and CD14⁻ phenotype, were undetectable in frozen samples.

Conclusion

These results suggest that optimization and evaluation of cryopreservation protocols is necessary for accurate biomarker discovery in frozen tumor specimens.

Electronic supplementary material

The online version of this article (doi:10.1186/s12865-017-0192-1) contains supplementary material, which is available to authorized users.

Inflammatory Manifestations of Lymphedema

Lymphedema results from lymphatic insufficiency leading to a progressive inflammatory process that ultimately manifests as discomfort, recurrent infections, and, at times, secondary malignancy. Collectively, these morbidities contribute to an overall poor quality of life. Although there have been recent advances in microsurgical interventions, a conservative palliative approach remains the mainstay of treatment for this disabling disease. The absence of a cure is due to an incomplete understanding of the pathophysiological changes that result in lymphedema. A histological hallmark of lymphedema is inflammatory cell infiltration and recent studies with animal models and clinical biopsy specimens have suggested that this response plays a key role in the pathology of the disease. The purpose of this report is to provide an overview of the ongoing research in and the current understanding of the inflammatory manifestations of lymphedema.

Drafting biological material transfer agreement: a ready-to-sign model for biobanks and biorepositories

PURPOSE

Due to the scarcity of publications, guidelines, and harmonization among national regulations, biobanks and institutions face practical and theoretical issues when drafting a material transfer agreement (MTA), the fundamental tool to regulate the successful exchange of biosamples and information. Frequently researchers do not execute MTAs because of a general lack of knowledge about this topic. It is thus critical to develop new models to prevent loss of traceability and opportunities both for researchers and biobanks, their exposure to various risks, and delays in transferring biomaterials.

METHODS

Through the involvement of institutional groups and professionals with multidisciplinary expertise, we have drawn up a ready-to-sign MTA for the CRO-Biobank (the biobank of the National Cancer Institute, CRO, Aviano), a standardized template that can be employed as a ready-to-use model agreement.

RESULTS

The team identified the essential components to be included in the MTA, which comprise i) permissions, liability and representations; ii) custodianship and distribution limitations; iii) appropriate use of materials, including biosafety concerns; iv) confidentiality, non-disclosure, and publications; v) intellectual property protection for both the provider and recipient.

CONCLUSIONS

This paper aims to be an unabridged report (among the few works in the existing literature) providing a description of the whole process related to the formation of an MTA. Biobanks and institutions may consider adopting our ready-to-sign form as a standard model. The article discusses the most important issues tackled during the drafting of the document, thus proposing an operative approach for other institutions that face the same problems.

Quality management of biorepositories

Biomedical investigators require high quality human tissue to support their research; thus, an important aspect of the provision of tissues by biorepositories is the assurance of high quality and consistency of processing specimens. This is best accomplished by a quality management system (QMS). This article describes the basis of a QMS program designed to aid biorepositories that want to improve their operations. In 1983, the UAB Tissue Collection and Biobanking Facility (TCBF) introduced a QMS program focused on providing solid tissues to support a wide range of research; this QMS included a quality control examination of the specific specimens provided for research. Similarly, the Division of Laboratory Sciences at the Centers for Disease Control and Prevention (CDC) introduced a QMS program for their laboratory analyses, focused primarily on bodily fluids. The authors of this article bring together the experience of the QMS programs at these two sites to facilitate the development or improvement of quality management systems of a wide range of biorepositories.

[Maintainance of a research tissue bank. (Infra)structural and quality aspects]

The availability of high quality human tissue samples and access to associated histopathological and clinical data are essential for biomedical research. Therefore, it is necessary to establish quality assured tissue biobanks that provide high quality tissue samples for research purposes. This entails quality concerns referring not only to the biomaterial specimen itself but encompassing all procedures related to biobanking, including the implementation of structural components, e.g. ethical and legal guidelines, quality management documentation as well as data and project management and information technology (IT) administration. Moreover, an integral aspect of tissue biobanks is the quality assured evaluation of every tissue specimen that is stored in a tissue biobank and used for projects to guarantee high quality assured biomaterial.

Challenges for quality management in implementation, maintenance, and sustainability of research tissue biobanks

Availability of high-quality human tissue samples and access to associated histopathological and clinical data is essential for basic and translational biomedical research, especially in areas of personalized medicine, drug, and biomarker development and mechanistically oriented biomedical research projects. Therefore, it is pivotal to establish and maintain quality-assured tissue biobanks that provide high-quality biomaterial to research thereby increasing the impact and reliability of scientific results. Quality concerns do not only address the biomaterial specimen itself but include all biobanking-related procedures. Tissue biobanks thus face essential challenges that encompass the implementation of adequate structural components, documentation of tissue sample collection and storage (procedures), as well as data and project management and IT. An integral and indispensable component of tissue biobanks is expert-driven evaluation (entry and exit controls) of tissue specimen to guarantee provision of high-quality assured biomaterials.

Oncology patients overwhelmingly support tissue banking

Background

Translational biomedical research relies on the availability of human tissue to explore disease aetiology and prognostic factors, with the objective of developing better targeted treatments. The establishment of biobanks poses ongoing ethical considerations in relation to donors. This is a quantitative study exploring medical oncology patients’ preferences for contributing to tissue biobanks.

Methods

The objectives of this study were to explore oncology patients’ preferences about tissue banking, including: 1) willingness to donate; 2) factors influencing donation decisions; 3) preferences about the use of donated tissue including permission systems, data linkage, and communication about research findings to donors. A cross-sectional survey was conducted in two tertiary oncology outpatient clinics. Eligible patients were approached by volunteers to complete a touchscreen survey in waiting rooms or while receiving intravenous therapy. Consenting participants completed demographic questions and received up to 12 previously validated items exploring preferences for donating tissue.

Results

224 oncology outpatients participated over a ten month period (69.1 % consent rate; 64.4 % completion rate). Most participants were female (54 %), were a mean age of 62 years, and diagnosed with breast (26 %) and bowel (20 %) cancer. Most participants indicated willingness to donate tissue (84 %) and for their sample to be stored for future use (96 %). Participants preferred a blanket consent approach (71 %), samples to be linked to medical records (62 %) and for general results of the research (79 %) to be provided to them. Factors influencing willingness to donate tissue included personal (85 %) or familial health benefits (88 %) and a sense of duty to future patients (82 %).

Conclusions

The overwhelming majority of oncology patients are willing to participate in a tissue bank, providing some support to explore ‘opt-out’ models of consent. To enhance patient acceptability, tissue banking programs should: (i) consider allowing blanket informed consent as well as opt-in models of consent; (ii) develop protocols allowing feedback of information about samples in line with patient preferences; (iii) provide clear information to potential donors about the benefits arising from donation.

Biobanking trends, challenges, and opportunities

OBJECTIVES

To review the different interests and needs of industry and academic users of human biomaterials.

METHODS

A review of the current literature and interviews with involved parties. Questionnaires were e-mailed to assess current attitudes towards biobanking and opinions of trends and implications for the future. The organisations included commercial biobanks, charitable foundations, academic biobanks, and hospital sites.

RESULTS

Biobanks have the potential to have a critical impact across several industrial sectors, and their future success will depend on satisfying the differing needs of each group. There is a growing need for greater collaboration between researchers and biobanks, and if the involvement of industry is not sought by biobanks to create conditions that support the effective use of resources, there is a risk that samples will not be collected or used to the best advantage.

CONCLUSIONS

It is evident that industry can play a vital role in the innovation process of biobanking, both in terms of the collecting and processing methods and the nature of the disease and sample types collected. With this feedback, biobanks can be utilised effectively to advance research to the benefits of all to the best advantage.

An online tool for improving biospecimen data element reporting

Detailed documentation of the experimental materials and methods is essential for the validation of scientific papers. Human biospecimens are increasingly utilized as materials in cancer research and information about the biospecimens used is a component of this documentation. We hypothesized that previously reported biospecimen data are inadequate for accurate replication and/or validation of a substantial proportion of studies. To examine this issue, we analyzed biospecimen reporting in a representative cross section of publications over the past 12 years (1998, 2004, 2010) in the journals, Cancer Research (CR, n=46) and Clinical Cancer Research (CCR, n=73). We assessed biospecimen data in relation to the standards outlined as the Tier 1 recommended data elements from the Biospecimen Reporting for Improved Study Quality (BRISQ), in addition to ethics criteria. These data elements encompass features of biospecimens influenced by the patient, medical procedure, and biospecimen acquisition, handling and storage processes. Analysis found that while there was a significant increase in the reporting of ethics board approval status (p<0.008) and name of the ethics board (p<0.0001), there were no significant differences between these journals or over this period in reporting other biospecimen-related data elements. Of the 15 Tier 1 data elements assessed in CR and CCR, the data elements commonly obtained from the "Clinical Chart" (8/15 elements) were significantly better reported than elements that would typically be obtained from the "Biobank" (p<0.0001). Our findings demonstrate that reporting of biospecimen-related data elements has been incomplete. As one part of the solution to this issue, we propose the use of an online data-elements reporting tool (www.biobanking.ca) by biobanks. This BRISQ Report tool aims to help biobanks provide the relevant biospecimen-related data as a structured report, and to promote its inclusion as supplementary material in publications to improve the quality of future research studies.

Establishment and management of a lung cancer biobank in Eastern China

Background

The prevalence of lung cancer, a highly complex neoplasm, increases annually. Thus, a lung cancer biobank, which stores lung cancer tissue and blood matched according to standard methods, is needed to advance lung cancer research and develop promising therapies.

Methods

To accomplish this aim, we implemented standardized procedures for tissue samples and patient information acquired from consenting donors. The banked tissue includes blood, pleural effusions, and surgical resection samples. An independent information management system was used to match samples and collect data, including clinical cancer manifestation, laboratory tests, and de-identified data about cancer patients.

Results

From 2009 to 2013, more than 2000 lung cancer cases were collected. At this time, we have more than 10 000 biological samples stored in our biobank. DNA, ribonucleic acid (RNA), and protein quality were confirmed to be appropriate for clinical and basic research.

Conclusion

Our standardized, large-scale lung cancer biobank offers high quality cancer research samples for China and the world.

Long-term storage of endocrine tissues at - 80°C does not adversely affect RNA quality or overall histomorphology

BACKGROUND

Today, no consensus exists regarding how human tissues are best preserved for long-term storage. Very low temperature storage in liquid nitrogen is often advocated as the superlative method for extended periods, but storage in -80 degrees Celsius (-80°C) freezers, while sometimes debated, is a possible alternative. RNA is the most easily degradable component of a biological sample in a molecular biology context and the quality can reliably be measured.

AIM

To investigate to what extent long-term storage of tissues in -80°C affects the RNA quality and overall histomorphology. The tissue storage period represents nearly three decades (1986-2013).

METHODS

RNA extraction from 153 tissue samples with different storage periods was performed with the mirVana kit (Invitrogen). RNA integrity was assessed using an Agilent bioanalyzer to obtain RNA integrity numbers (RIN). Further, tissue representative testing using light microscopy was performed by two pathologists to assess tissue composition and morphology.

RESULTS

RIN values were measured in all samples, showing a variability that did not correlate with the storage time of the tissues. Microscopically, all samples displayed acceptable tissue morphology regardless of storage time.

CONCLUSION

Long-term storage in -80°C does not adversely affect the quality of the RNA extracted from the stored tissues, and the tissue morphology is maintained to a good standard.

Digital pathology and image analysis augment biospecimen annotation and biobank quality assurance harmonization

Standardization of biorepository best practices will enhance the quality of translational biomedical research utilizing patient-derived biobank specimens. Harmonization of pathology quality assurance procedures for biobank accessions has lagged behind other avenues of biospecimen research and biobank development. Comprehension of the cellular content of biorepository specimens is important for discovery of tissue-specific clinically relevant biomarkers for diagnosis and treatment. While rapidly emerging technologies in molecular analyses and data mining create focus on appropriate measures for minimizing pre-analytic artifact-inducing variables, less attention gets paid to annotating the constituent makeup of biospecimens for more effective specimen selection by biobank clients. Both pre-analytic tissue processing and specimen composition influence acquisition of relevant macromolecules for downstream assays. Pathologist review of biorepository submissions, particularly tissues as part of quality assurance procedures, helps to ensure that the intended target cells are present and in sufficient quantity in accessioned specimens. This manual procedure can be tedious and subjective. Incorporating digital pathology into biobank quality assurance procedures, using automated pattern recognition morphometric image analysis to quantify tissue feature areas in digital whole slide images of tissue sections, can minimize variability and subjectivity associated with routine pathologic evaluations in biorepositories. Whole-slide images and pathologist-reviewed morphometric analyses can be provided to researchers to guide specimen selection. Harmonization of pathology quality assurance methods that minimize subjectivity and improve reproducibility among collections would facilitate research-relevant specimen selection by investigators and could facilitate information sharing in an integrated network approach to biobanking.

A biorepository for ophthalmic surgical specimens

Biorepositories are collections of surgically obtained human tissues for current and future investigations of disease mechanisms, therapeutics, and diagnostics. In ophthalmology, a critical challenge is how to interface the operating room with the laboratory. To attain standards required for basic research, clinical and research teams must cooperate to collect, annotate, and store specimens that yield consistent results required for advanced molecular techniques. We developed an efficient platform for obtaining vitreous and other eye tissues from the operating room and transferring them to the lab. The platform includes a mobile lab cart for on-site tissue processing, a multi-user, web-based database for point-of-care phenotypic capture, and an integrated data tracking system for long-term storage. These biorepository instruments have proven essential for our studies in ophthalmic disease proteomics. This system can be implemented in other operating rooms and laboratories for a variety of biological tissues.

Challenges in biobank governance in Sub-Saharan Africa

BACKGROUND

Biological sample and data transfer within and out of Africa is steeped in controversy With the H3Africa project now aiming to establish biobanks in Africa, it is essential that there are ethical and legal governance structures in place to oversee the operation of these biobanks. Such governance is essential to ensuring that donors are protected, that cultural perspectives are respected and that researchers have a ready availability of ethically sourced biological samples.

METHODS

A literature review of all legislation, regulations, guidelines and standard operating procedures on informed consent, confidentiality and the transfer of biological samples amongst countries in Sub-Saharan Africa was conducted. In addition, an examination of the websites of departments of health and national ethics committees was performed. Researchers and research ethics scholars in the field in various African countries were contacted for assistance. A literature review of all studies examining participants views on issues related to biobanking in Africa was carried out and five separate studies were found.

RESULTS

It was found that biobanking guidelines differ substantially across Sub-Saharan Africa regarding biobanking and often conflicted across borders. This has the potential to negatively impact collaboration. Furthermore, the guidelines in place often do not recognise the ethical difficulties arising from the transfer of biological samples and are unsuitable to regulate biobanks. Additionally, there is insufficient research into the views of research participants and stakeholders on the use of biological /samples.

CONCLUSION

Collaboration is necessary to ensure the success of biobanking projects in Africa. To achieve this, there should be some harmonization of guidelines across Africa which would aid in transferring biological samples across borders. These guidelines should reflect the unique ethical issues arising out of the storage and secondary uses of biological samples. Finally, further research into the views of research participants is necessary. Such studies should aid in the drafting of any new harmonization guidelines.

Use of human specimens in research: the evolving United States regulatory, policy, and scientific landscape

The use of human specimens in research has contributed to significant scientific and medical advancements. However, the development of sophisticated whole genome and informatics technologies and the increase in specimen and data sharing have raised new questions about the identifiability of specimens and the protection of participants in human specimen research. In the US, new regulations and policies are being considered to address these changes. This review discusses the current and proposed regulations as they apply to specimen research, as well as relevant policy discussions. It summarizes the ways that researchers and other stakeholders can provide their input to these discussions and policy development efforts. Input from all the stakeholders in specimen research will be essential for the development of policies that facilitate such research while at the same time protecting the rights and welfare of research participants.

Surgeon leadership enables development of a colorectal cancer biorepository

BACKGROUND

We hypothesized that surgeons can improve the collection of all necessary elements (tissue and clinical data) needed to build a complete, robust research biorepository.

METHODS

All colorectal cancer patients treated at a university medical center and its affiliates were eligible for inclusion. Data were collected from an 18-page personal and family health questionnaire, a prospectively maintained clinical database, and molecular testing. Tissues included serum, plasma and peripheral blood mononuclear cells, and tumor and normal tissue. We compared 2 groups: the surgeon-referred group and the other clinician-referred group. The primary outcome was the complete collection of data (ie, preoperative/staging clinical data, blood samples, and tissue collection). Statistical analysis was performed using the Student t test.

RESULTS

Since 2006, 452 patients were approached, and 430 (95%) have been enrolled. Of these, 124 were referred by their surgeon, and 306 were consented in a clinic or over the telephone. Of patients referred by their surgeon, tumor tissue, blood samples, and preoperative/staging clinical data were obtained in 119 patients; conversely, in patients referred by oncologists or other clinicians, only 133 patients had complete data (96% vs 43.5%, P < .05). A total of 257 tissue samples were obtained from all patients. Additional testing has been performed on 228 specimens including immunohistochemistry, microsatellite testing, and genotype mutational analysis.

CONCLUSIONS

Surgeon-directed enrollment in a biorepository improves the ability to collect blood and tissue samples. Surgeons should take a leadership role in the development of tumor biorepositories.

The prognostic value of microRNAs varies with patient race/ethnicity and stage of colorectal cancer

PURPOSE

MicroRNAs (miRNA) have potential prognostic value for colorectal cancers; however, their value based on patient race/ethnicity and pathologic stage has not been determined. The goal was to ascertain the prognostic value of 5 miRNAs with increased expression in colorectal cancers of African American (black) and non-Hispanic Caucasian (white) patients.

EXPERIMENTAL DESIGN

TaqMan quantitative real-time PCR was used to quantify expression of miR-20a, miR-21, miR-106a, miR-181b, and miR-203 in paired normal and tumor colorectal cancer archival tissues collected from 106 black and 239 white patients. The results were correlated with overall survival based on patient race/ethnicity and pathologic stage. Because decisions about adjuvant therapy are important for stage III colorectal cancers, and because miR-181b seemed to have prognostic value only for stage III black patients, we assessed its prognostic value in a separate cohort of 36 stage III colorectal cancers of blacks.

RESULTS

All 5 miRNAs had higher expression in colorectal cancers (>1.0-fold) than in corresponding normal tissues. High expression of miR-203 was associated with poor survival of whites with stage IV colorectal cancers (HR = 3.00; 95% CI, 1.29-7.53), but in blacks it was an indicator of poor survival of patients with stages I and II colorectal cancers (HR = 5.63; 95% CI, 1.03-30.64). Increased miR-21 expression correlated with poor prognosis for white stage IV patients (HR = 2.50; 95% CI, 1.07-5.83). In both test and validation cohorts, high miR-181b expression correlated with poor survival of only black patients with stage III colorectal cancers (HR = 1.94; 95% CI, 1.03-3.67).

CONCLUSION

These preliminary findings suggest that the prognostic value of miRNAs in colorectal cancers varies with patient race/ethnicity and stage of disease.