An estimated 15% or more of the cancer burden worldwide is attributable to known infectious agents. We screened colorectal carcinoma and matched normal tissue specimens using RNA-seq followed by host sequence subtraction and found marked over-representation of Fusobacterium nucleatum sequences in tumors relative to control specimens. F. nucleatum is an invasive anaerobe that has been linked previously to periodontitis and appendicitis, but not to cancer. Fusobacteria are rare constituents of the fecal microbiota, but have been cultured previously from biopsies of inflamed gut mucosa. We obtained a Fusobacterium isolate from a frozen tumor specimen; this showed highest sequence similarity to a known gut mucosa isolate and was confirmed to be invasive. We verified overabundance of Fusobacterium sequences in tumor versus matched normal control tissue by quantitative PCR analysis from a total of 99 subjects ( p = 2.5 3 10 -6), and we observed a positive association with lymph node metastasis.[Supplemental material is available for this article.] There are variations on the method, but the basic approach involves shotgun sequencing bulk DNA or RNA isolated from disease tissue, computational subtraction of all sequence reads recognized as human, and comparison of the residual reads to databases of known microbial sequences in order to identify microbial species present in the initial specimen. The method is complementary to traditional culture and histolology-based protocols, and new massively parallel sequencing technologies impart high sensitivity. At present the power of the method remains restricted by the content of microbial sequence databases, but with our increasing reach into microbial sequence space, the comprehensiveness of these data resources continues to improve. In oncology, the identification of a novel polyomavirus in Merkel Cell carcinoma (Feng et al. 2008) is a recent demonstration of the utility of a metagenomics approach.Colorectal carcinoma (CRC) is the fourth leading cause of cancer deaths, responsible for approximately 610,000 deaths per year worldwide (World Health Organization 2011). It is also one of the first and best genetically characterized cancers, and specific somatic mutations in oncogenes and tumor suppressor genes have been found that are associated with progression from adenomatous lesions (polyps) to invasive carcinoma (Vogelstein et al. 1988). The root cause of CRC is unclear, but inflammation is a well-recognized risk factor (Wu et al. 2009;McLean et al. 2011). Given the link between H. pylori-mediated inflammation and gastric cancer (Marshall and Warren 1984), we asked if inflammatory microorganisms are associated with other gastrointestinal (GI) cancers. We began to address this question by undertaking a metagenomic survey of colorectal carcinoma. ResultsTotal RNA was isolated from frozen sections of 11 matched pairs of colorectal carcinoma and adjacent normal tissue specimens. RNA was purified by host ribosomal sequence depletion, rather than poly(A) selection, in order to re...

BackgroundTumor-infiltrating T cells are associated with survival in epithelial ovarian cancer (EOC), but their functional status is poorly understood, especially relative to the different risk categories and histological subtypes of EOC.Methodology/Principal FindingsTissue microarrays containing high-grade serous, endometrioid, mucinous and clear cell tumors were analyzed immunohistochemically for the presence of lymphocytes, dendritic cells, neutrophils, macrophages, MHC class I and II, and various markers of activation and inflammation. In high-grade serous tumors from optimally debulked patients, positive associations were seen between intraepithelial cells expressing CD3, CD4, CD8, CD45RO, CD25, TIA-1, Granzyme B, FoxP3, CD20, and CD68, as well as expression of MHC class I and II by tumor cells. Disease-specific survival was positively associated with the markers CD8, CD3, FoxP3, TIA-1, CD20, MHC class I and class II. In other histological subtypes, immune infiltrates were less prevalent, and the only markers associated with survival were MHC class II (positive association in endometrioid cases) and myeloperoxidase (negative association in clear cell cases).Conclusions/SignificanceHost immune responses to EOC vary widely according to histological subtype and the extent of residual disease. TIA-1, FoxP3 and CD20 emerge as new positive prognostic factors in high-grade serous EOC from optimally debulked patients.

Each year funding agencies and academic institutions spend millions of dollars and euros on biobanking. All funding providers assume that after initial investments biobanks should be able to operate sustainably. However the topic of sustainability is challenging for the discipline of biobanking for several major reasons: the diversity in the biobanking landscape, the different purposes of biobanks, the fact that biobanks are dissimilar to other research infrastructures and the absence of universally understood or applicable value metrics for funders and other stakeholders. In this article our aim is to delineate a framework to allow more effective discussion and action around approaches for improving biobank sustainability. The term sustainability is often used to mean fiscally self-sustaining, but this restricted definition is not sufficient for biobanking. Instead we propose that biobank sustainability should be considered within a framework of three dimensions - financial, operational, and social. In each dimension, areas of focus or elements are identified that may allow different types of biobanks to distinguish and evaluate the relevance, likelihood, and impact of each element, as well as the risks to the biobank of failure to address them. Examples of practical solutions, tools and strategies to address biobank sustainability are also discussed.

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Human research biobanks have rapidly expanded in the past 20 years, in terms of both their complexity and utility. To date there exists no agreement upon classification schema for these biobanks. This is an important issue to address for several reasons: to ensure that the diversity of biobanks is appreciated, to assist researchers in understanding what type of biobank they need access to, and to help institutions/funding bodies appreciate the varying level of support required for different types of biobanks. To capture the degree of complexity, specialization, and diversity that exists among human research biobanks, we propose here a new classification schema achieved using a conceptual classification approach. This schema is based on 4 functional biobank "elements" (donor/participant, design, biospecimens, and brand), which we feel are most important to the major stakeholder groups (public/participants, members of the biobank community, health care professionals/researcher users, sponsors/funders, and oversight bodies), and multiple intrinsic features or "subelements" (eg, the element "biospecimens" could be further classified based on preservation method into fixed, frozen, fresh, live, and desiccated). We further propose that the subelements relating to design (scale, accrual, data format, and data content) and brand (user, leadership, and sponsor) should be specifically recognized by individual biobanks and included in their communications to the broad stakeholder audience.

Demand for biospecimens in cancer research has increased but there are relatively few data on the trends in biospecimen usage. These data are needed to enable projection of future demand. We analyzed biospecimen usage in publications published at five-year intervals (2008, 2003, 1998, 1993, and 1988) in four cancer research journals (Cancer Research, Clinical Cancer Research, British Journal of Cancer and International Journal of Cancer). We categorized publications in three ways: 1) biospecimen utilization yes/no; 2) biospecimen cohort size; and 3) format of biospecimens used including frozen tissue, Formalin-Fixed Paraffin-Embedded (FFPE) tissue, fresh tissue, fluids, and hematological biospecimens. Biospecimens were used in 1292/3307 (39%) of publications analyzed and sufficient information was available to further classify biospecimen usage in 1228 publications. The proportion of publications in each journal using biospecimens ranged from 23% to 61% between journals, with no significant change within each journal over time. A more detailed review of tissue biospecimen use showed a significant increase in cohort sizes from 1988 to 2008 (mean 52 to 198, respectively; P < 0.0001). This reflected increased cohort sizes for both frozen and FFPE tissues from 1993 to 2008 (frozen, 59 to 119; FFPE, 66 to 194) but not fresh tissues. The relative proportion of studies using frozen or fresh tissues alone has decreased (71% to 24%) while those using FFPE alone or combined FFPE/frozen tissue cohorts has increased (24% to 72%) over this period. We conclude that the overall demand for biospecimens in cancer research has increased significantly (almost fourfold) over the past 20 years. We predict that average cohort sizes will increase by at least twofold for frozen and FFPE biospecimens over the next ten years, and that the majority of studies will be based on FFPE tissues or combined FFPE/Frozen tissue cohorts.

BackgroundMedical research to improve health care faces a major problem in the relatively limited availability of adequately annotated and collected biospecimens. This limitation is creating a growing gap between the pace of scientific advances and successful exploitation of this knowledge. Biobanks are an important conduit for transfer of biospecimens (tissues, blood, body fluids) and related health data to research. They have evolved outside of the historical source of tissue biospecimens, clinical pathology archives. Research biobanks have developed advanced standards, protocols, databases, and mechanisms to interface with researchers seeking biospecimens. However, biobanks are often limited in their capacity and ability to ensure quality in the face of increasing demand. Our strategy to enhance both capacity and quality in research biobanking is to create a new framework that repatriates the activity of biospecimen accrual for biobanks to clinical pathology.MethodsThe British Columbia (BC) BioLibrary is a framework to maximize the accrual of high-quality, annotated biospecimens into biobanks. The BC BioLibrary design primarily encompasses: 1) specialized biospecimen collection units embedded within clinical pathology and linked to a biospecimen distribution system that serves biobanks; 2) a systematic process to connect potential donors with biobanks, and to connect biobanks with consented biospecimens; and 3) interdisciplinary governance and oversight informed by public opinion.ResultsThe BC BioLibrary has been embraced by biobanking leaders and translational researchers throughout BC, across multiple health authorities, institutions, and disciplines. An initial pilot network of three Biospecimen Collection Units has been successfully established. In addition, two public deliberation events have been held to obtain input from the public on the BioLibrary and on issues including consent, collection of biospecimens and governance.ConclusionThe BC BioLibrary framework addresses common issues for clinical pathology, biobanking, and translational research across multiple institutions and clinical and research domains. We anticipate that our framework will lead to enhanced biospecimen accrual capacity and quality, reduced competition between biobanks, and a transparent process for donors that enhances public trust in biobanking.

Purpose: Translational cancer research increasingly relies on human tissue biospecimens and this has coincided with a shift in tissue biobanking approach. Newer biobanks (post year 2000) deploy standard operating procedures to reduce variability around biospecimen collection. Because current translational research is based on pre-2000 and post-2000 era biospecimens, we consider whether the collection era may influence gene expression data. Design: We compared the range of breast tumor collection times from pre-2000 and post-2000 era biobanks and compared estrogen receptor (ER) protein expression with collection time. We then collected 10 breast tumor biospecimens under a standardized protocol and examined whether the expression of c-myc and ER was influenced by storage on ice ≤24 hours. Results: The range of collection times achieved at a pre-2000 versus post-2000 era biobank differed. Thirty-two percent of biospecimens were cryopreserved within 30 minutes at the pre-2000 era biobank versus 76% at the post-2000 era biobank. Collection time and ER protein level was inversely correlated (r = −0.19, P = 0.025; n = 137). We observed a wide range in initial c-myc and ER mRNA levels (50- versus 130-fold). Although mRNA levels of both genes declined with increasing collection time, the rate of change differed because c-myc was significantly reduced after 24 hours (mean reduction to 79% of initial) versus ER (94% of initial). Conclusion: The overall shift in biobanking around the year 2000 is reflected in the ranges of collection times associated with pre-2000 and post-2000 era biobanks. Because collection time can differentially alter gene expression, the biospecimen collection era should be considered in gene expression studies. (Cancer Epidemiol Biomarkers Prev 2008;17(12):3344–50)