Resource For Translational Research Research Articles

Living Biobanks of Organoids: Valuable Resource for Translational Research.

The emergence of organoids is considered a revolutionary model, changing the landscape of traditional translational research. These three-dimensional miniatures of human organs or tissues, cultivated from stem cells or biospecimens obtained from patients, faithfully replicate the structural and functional characteristics of specific target organs or tissues. In this extensive review, we explore the profound impact of organoids and assess the current state of living organoid biobanks, which are essential repositories for cryopreserving organoids derived from a variety of diseases. These resources hold significant value for translational research. We delve into the diverse origins of organoids, the underlying technologies, and their roles in recapitulating human development, disease modeling, as well as their potential applications in the pharmaceutical field. With a particular emphasis on biobanking organoids for prospective applications, we discuss how these advancements expedite the transition from bench to bedside translational research, thereby fostering personalized medicine and enriching our comprehension of human health.

Abstract 6915: Integrated proteogenomic analysis for the NCI patient-derived cancer model repository

Abstract Background: Studying protein expression involved in cancer from patient-derived xenografts (PDX) enhances understanding of tumorigenesis and may shed light on patient therapeutic decisions. Recently, mass spectrometry-based proteomics sequencing techniques have enabled the acquisition of high-throughput PDX protein/phosphoprotein expression profiles and paved a way for investigating oncogenic signaling pathways and their interactions in different tumor histologies. Integrated analysis of these proteomic data with existing biomarkers derived from whole exome and RNAseq data will provide the community with a rich resource for translational research. Materials and methods: iTRAQ-based proteomics/phospho-proteomics data, with 11 Tandem Mass Tag (TMT) channels, were processed and median-normalized at gene level. The gene expression data were derived from tximport and DESeq2 from of RNA-Seq. In addition, whole exome sequencing (WES) data were used to compute mutations and copy number profiles. For data visualization, the R Bioconductor package ComplexHeatmap was used extensively. Results: PDX proteomics/phospho-proteomics data were analyzed alongside with gene expression, copy number and mutational profiles for several cancer types, revealing vivid molecular regulation for many cancer-related pathways. A moderate yet significant Spearman correlation coefficient of over 0.45 and 0.5 was observed between proteomics and RNA-Seq data at gene and pathway level, respectively. The PDX protein and gene expression pattern from common cancer regulatory pathways of bladder (BLCA, n=32 models), colon (COAD, n=82), lung (NSCLC, n=32), pancreatic (PAAD, n=52), metastatic breast cancer (CSNOS) (n=16) and other histologies were aggregated and discussed at the model level. EGFR, MET and cell-cycle genes CDKN2A and CDKN2B exhibited significant positive correlation among copy number, gene expression and protein expression profiles. Protein and gene expression profiles of PAM50 genes were shown for CSNOS samples, to further sub-classify or correct misclassification. Further analysis using proteomics/phospho-proteomics data with CNA identified several trans-regulatory events. Lastly, we identified RTN1 as a potential biomarker, exhibiting lower expression in sensitive rare-tumor PDX models prior to Axitinib and Vandetanib treatment. Conclusions: With the multi-omics datasets comprising proteomics/phospho-proteomics, RNA-Seq and WES datasets from the NCI Patient Derived Models Repository cohort, we were able to query some important cancer biological processes at a higher resolution. In addition, we revealed gene- and pathway-level regulatory differences from various histologies. Overall, the multi-omics data from PDX models showed promising recapitulation of original tumor activity and should continue to serve as an amenable and scalable drug screening platform for pre-clinical trials. Citation Format: Peter I. Wu, Li Chen, Yuri Kotliarov, Jianwen Fang, Yingdong Zhao, Yvonne Evrard, Lijun Chen, Shahanawaz Jiwani, Biswajit Das, Chris A. Karlovich, Hui Zhang, Lisa McShane, Melinda G. Hollingshead, Mickey Williams, James H. Doroshow. Integrated proteogenomic analysis for the NCI patient-derived cancer model repository [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6915.

The value of subcutaneous xenografts for individualised radiotherapy in HNSCC: Robust gene signature correlates with radiotherapy outcome in patients and xenografts

PurposeTo assess the robustness of prognostic biomarkers and molecular tumour subtypes developed for patients with head and neck squamous cell carcinoma (HNSCC) on cell-line derived HNSCC xenograft models, and to develop a novel biomarker signature by combining xenograft and patient datasets. Materials and methodsMice bearing xenografts (n = 59) of ten HNSCC cell lines and a retrospective, multicentre patient cohort (n = 242) of the German Cancer Consortium-Radiation Oncology Group (DKTK-ROG) were included. All patients received postoperative radiochemotherapy (PORT-C). Gene expression analysis was conducted using GeneChip Human Transcriptome Arrays. Xenografts were stratified based on their molecular subtypes and previously established gene classifiers. The dose to control 50 % of tumours (TCD50) was compared between these groups. Using differential gene expression analyses combining xenograft and patient data, a gene signature was developed to define risk groups for the primary endpoint loco-regional control (LRC). ResultsTumours of mesenchymal subtype were characterized by a higher TCD50 (xenografts, p < 0.001) and lower LRC (patients, p < 0.001) compared to the other subtypes. Similar to previously published patient data, hypoxia- and radioresistance-related gene signatures were associated with high TCD50 values. A 2-gene signature (FN1, SERPINE1) was developed that was prognostic for TCD50 (xenografts, p < 0.001) and for patient outcome in independent validation (LRC: p = 0.007). ConclusionGenetic prognosticators of outcome for patients after PORT-C and subcutaneous xenografts after primary clinically relevant irradiation show similarity. The identified robust 2-gene signature may help to guide patient stratification, after prospective validation. Thus, xenografts remain a valuable resource for translational research towards the development of individualized radiotherapy.

Transitioning Electrochemical Technologies into Agriculture via the National Science Foundation Engineering Research Center Model

One of the most difficult challenges in translating electrochemical technologies into agriculture is the lag in education about the impact of electrochemical technologies in the field. Other challenges include lack of (1) investment and resources for translational research; (2) effective mechanisms to derisk investment; (3) a workforce prepared to translate and operate such technologies; (4) policy, legal infrastructure, and holistic business growth models; and (5) diverse and inclusive leadership “agents of change” to transition the technologies into the market. Opportunities to translate research into the market require strong partnerships with industry, universities, government, and stakeholders. An effective model is the National Science Foundation (NSF) Engineering Research Center (ERC) model. An NSF ERC Gen-4 launched in August 2022 is the Center for Advancing Sustainable and Distributed Fertilizer Production (CASFER). Industry and other practitioner organizations are actively involved at the very early stage (articulation of the vision) and during operation in activities such as: participation in strategic planning, joint research, providing input into workforce development programs, mentoring students, and engagement in proof-of-concept testbeds. All these activities and engagement are key to accelerating technology transfer and to transitioning technologies from the lab to the market, while training an effective workforce for industry.

The structural and functional integrities of porcine myocardium are mostly preserved by cryopreservation.

Structural and functional studies of heart muscle are important to gain insights into the physiological bases of cardiac muscle contraction and the pathological bases of heart disease. While fresh muscle tissue works best for these kinds of studies, this is not always practical to obtain, especially for heart tissue from large animal models and humans. Conversely, tissue banks of frozen human hearts are available and could be a tremendous resource for translational research. It is not well understood, however, how liquid nitrogen freezing and cryostorage may impact the structural integrity of myocardium from large mammals. In this study, we directly compared the structural and functional integrity of never-frozen to previously frozen porcine myocardium to investigate the consequences of freezing and cryostorage. X-ray diffraction measurements from hydrated tissue under near-physiological conditions and electron microscope images from chemically fixed porcine myocardium showed that prior freezing has only minor effects on structural integrity of the muscle. Furthermore, mechanical studies similarly showed no significant differences in contractile capabilities of porcine myocardium with and without freezing and cryostorage. These results demonstrate that liquid nitrogen preservation is a practical approach for structural and functional studies of myocardium.

Phenomenology as a resource for translational research in mental health: methodological trends, challenges and new directions.

This editorial reflects on current methodological trends in translational research in mental health. It aims to build a bridge between two fields that are frequently siloed off from each other: interventional research and phenomenologically informed research. Recent years have witnessed a revival of phenomenological approaches in mental health, often - but not only - as a means of connecting the subjective character of experience with neurobiological explanatory accounts of illness. Rich phenomenological knowledge accrued in schizophrenia, and wider psychosis research, has opened up new opportunities for improving prediction, early detection, diagnosis, prognostic stratification, treatment and ethics of care. Novel qualitative studies of delusions and hallucinations have challenged longstanding assumptions about their nature and meaning, uncovering highly complex subjective dimensions that are not adequately captured by quantitative methodologies. Interdisciplinary and participatory research efforts, informed by phenomenological insights, have prompted revisions of pre-established narratives of mental disorder dominated by a dysfunction framework and by researcher-centric outcome measures. Despite these recent advances, there has been relatively little effort to integrate and translate phenomenological insights across applied clinical research, with the goal of producing more meaningful, patient-valued results. It is our contention that phenomenological psychopathology - as the basic science of psychiatry - represents an important methodology for advancing evidence-based practices in mental health, and ultimately improving real-world outcomes. Setting this project into motion requires a greater emphasis on subjectivity and the structures of experience, more attention to the quality and patient-centredness of outcome measures, and the identification of treatment targets that matter most to patients.

International Spinal Cord Injury Biobank: A Biorepository and Resource for Translational Research.

Over the past few decades, tremendous advances have been made in our understanding of the biological changes underpinning the devastating impairment of traumatic spinal cord injury (SCI). Much of this scientific research has focused on animal models of SCI, and comparatively little has been done in human SCI, largely because biospecimens from human SCI patients are not readily available. This paucity of scientific enquiry in human SCI represents an important void in the spectrum of translational research, as biological differences between animal models and the human condition need to be considered in the pre-clinical development of therapeutic approaches. The International Spinal Cord Injury Biobank (ISCIB) is a multi-user biorepository with the mission of accelerating therapeutic development in traumatic SCI through improved biological understanding of human injury, and the vision of serving as a global research resource where human SCI biospecimens are shared with researchers around the world. Aligned with internationally recognized best practices, ISCIB's formal governance structure and standard operating procedures have earned it official biobank certification through the Canadian Tissue Repository Network. Herein, we describe the translational research gap that ISCIB is helping to fill; its structure, governance and certification; how data and samples are accrued, processed and stored; and finally, the process through which samples and data are shared with global researchers. The purpose of this paper describing ISCIB is to serve as an introductory guidance document for the wider community of SCI researchers. By helping researchers understand the contents of ISCIB and the process of accessing biospecimens, we seek to further ISCIB's vision as being a resource for human and translational research in SCI, with the ultimate goal of finding disease-modifying therapies for this disabling condition.

Comprehensive profiling of 1015 patients\u2019 exomes reveals genomic-clinical associations in colorectal cancer

The genetic basis of colorectal cancer (CRC) and its clinical associations remain poorly understood due to limited samples or targeted genes in current studies. Here, we perform ultradeep whole-exome sequencing on 1015 patients with CRC as part of the ChangKang Project. We identify 46 high-confident significantly mutated genes, 8 of which mutate in 14.9% of patients: LYST, DAPK1, CR2, KIF16B, NPIPB15, SYTL2, ZNF91, and KIAA0586. With an unsupervised clustering algorithm, we propose a subtyping strategy that classisfies CRC patients into four genomic subtypes with distinct clinical characteristics, including hypermutated, chromosome instability with high risk, chromosome instability with low risk, and genome stability. Analysis of immunogenicity uncover the association of immunogenicity reduction with genomic subtypes and poor prognosis in CRC. Moreover, we find that mitochondrial DNA copy number is an independent factor for predicting the survival outcome of CRCs. Overall, our results provide CRC-related molecular features for clinical practice and a valuable resource for translational research.

Patient-Derived Organoids of Cholangiocarcinoma.

Cholangiocarcinoma (CC) is an aggressive malignancy with an inferior prognosis due to limited systemic treatment options. As preclinical models such as CC cell lines are extremely rare, this manuscript reports a protocol of cholangiocarcinoma patient-derived organoid culture as well as a protocol for the transition of 3D organoid lines to 2D cell lines. Tissue samples of non-cancer bile duct and cholangiocarcinoma were obtained during surgical resection. Organoid lines were generated following a standardized protocol. 2D cell lines were generated from established organoid lines following a novel protocol. Subcutaneous and orthotopic patient-derived xenografts were generated from CC organoid lines, histologically examined, and treated using standard CC protocols. Therapeutic responses of organoids and 2D cell lines were examined using standard CC agents. Next-generation exome and RNA sequencing was performed on primary tumors and CC organoid lines. Patient-derived organoids closely recapitulated the original features of the primary tumors on multiple levels. Treatment experiments demonstrated that patient-derived organoids of cholangiocarcinoma and organoid-derived xenografts can be used for the evaluation of novel treatments and may therefore be used in personalized oncology approaches. In summary, this study establishes cholangiocarcinoma organoids and organoid-derived cell lines, thus expanding translational research resources of cholangiocarcinoma.

Mini-Review of Laboratory Operations in Biobanking: Building Biobanking Resources for Translational Research.

Biobanks have become integral to improving population health. We are in a new era in medicine as patients, health professionals, and researchers increasingly collaborate to gain new knowledge and explore new paradigms for diagnosing and treating disease. Many large-scale biobanking efforts are underway worldwide at the institutional, national, and even international level. When linked with subject data from questionnaires and medical records, biobanks serve as valuable resources in translational research. A biobank must have high quality samples that meet researcher's needs. Biobank laboratory operations require an enormous amount of support—from lab and storage space, information technology expertise, and a laboratory management information system to logistics for sample movement, quality management systems, and appropriate facilities. A paramount metric of success for a biobank is the concept of every biospecimen coming to the repository belongs to a participant who has something to contribute to research for a healthier future. This article will discuss the importance of biorepository operations, specific to the collection and storage of participants materials. Specific focus will be given to maintaining the quality of samples, along with the various levels of support biorepositories need to fulfill their purpose and ensure the integrity of each specimen is maintained.

An Economic Dilemma Between Molecular Weapon Systems May Explain an Arachno-atypical Venom in Wasp Spiders (Argiope bruennichi).

Spiders use venom to subdue their prey, but little is known about the diversity of venoms in different spider families. Given the limited data available for orb-weaver spiders (Araneidae), we selected the wasp spider Argiope bruennichi for detailed analysis. Our strategy combined a transcriptomics pipeline based on multiple assemblies with a dual proteomics workflow involving parallel mass spectrometry techniques and electrophoretic profiling. We found that the remarkably simple venom of A. bruennichi has an atypical composition compared to other spider venoms, prominently featuring members of the cysteine-rich secretory protein, antigen 5 and pathogenesis-related protein 1 (CAP) superfamily and other, mostly high-molecular-weight proteins. We also detected a subset of potentially novel toxins similar to neuropeptides. We discuss the potential function of these proteins in the context of the unique hunting behavior of wasp spiders, which rely mostly on silk to trap their prey. We propose that the simplicity of the venom evolved to solve an economic dilemma between two competing yet metabolically expensive weapon systems. This study emphasizes the importance of cutting-edge methods to encompass the lineages of smaller venomous species that have yet to be characterized in detail, allowing us to understand the biology of their venom systems and to mine this prolific resource for translational research.

Modeling rectal cancer to advance neoadjuvant precision therapy

Progress in rectal cancer therapy has been hindered by the lack of effective disease-specific preclinical models that account for the unique molecular profile and biology of rectal cancer. Thus, we developed complementary patient-derived xenograft (PDX) and subsequent in vitro tumor organoid (PDTO) platforms established from preneoadjuvant therapy rectal cancer specimens to advance personalized care for rectal cancer patients. Multiple endoscopic samples were obtained from 26 Stages 2 and 3 rectal cancer patients prior to receiving 5FU/RT and implanted subcutaneously into NSG mice to generate 15 subcutaneous PDXs. Second passaged xenografts demonstrated 100% correlation with the corresponding human cancer histology with maintained mutational profiles. Individual rectal cancer PDXs reproduced the 5FU/RT response observed in the corresponding human cancers. Similarly, rectal cancer PDTOs reproduced significant heterogeneity in cellular morphology and architecture. PDTO in vitro 5FU/RT treatment response replicated the clinical 5FU/RT neoadjuvant therapy pathologic response observed in the corresponding patient tumors (p < 0.05). The addition of cetuximab to the 5FU/RT regiment was significantly more sensitive in the rectal cancer PDX and PDTOs with wild-type KRAS compared to mutated KRAS (p < 0.05). Considering the close relationship between the patient's cancer and the corresponding PDX/PDTO, rectal cancer patient-derived research platforms represent powerful translational research resources as population-based tools for biomarker discovery and experimental therapy testing. In addition, our findings suggest that cetuximab may enhance RT effectiveness by improved patient selection based on mutational profile in addition to KRAS or by developing a protocol using PDTOs to identify sensitive patients.

Building capacity for dissemination and implementation to maximize research impact in a CTSA: The University of Wisconsin story.

We report results of an 8-year process of stakeholder engagement aimed at building capacity in Dissemination and Implementation (D&I) research at the University of Wisconsin as part of the National Institutes of Health's Clinical and Translational Science Award (CTSA). Starting in 2008, annual individual interviews were held with leaders of the Wisconsin CTSA's community engagement core for strategic planning purposes. Interviews were followed by annual planning meetings that employed a facilitated group decision-making process aimed at identifying and prioritizing gaps in the translational research spectrum. In 2011, the stakeholder engagement process identified D&I as a primary gap limiting overall impact of the institution's research across the translational spectrum. Since that time, our CTSA has created an array of D&I resources falling into four broad categories: (1) relationship building with D&I partners, (2) D&I skill building, (3) translational research resources, and (4) resources to support D&I activities. Our systematic process of stakeholder engagement has increased the impact of research by providing D&I resources to meet investigator and community needs. CTSAs could engage with leaders of their community engagement cores, which are common to all CTSAs, to adapt or adopt these resources to build D&I capacity.

High-Quality Biobanks: Pivotal Assets for Reproducibility of OMICS-Data in Biomedical Translational Research.

Human biospecimen samples (HBS) and associated data stored in biobanks (also called "biotrusts," "biorepositories," or "biodistributors") are very critical resources for translational research. As HBS quality is decisive to the reproducibility of research results, biobanks are also key assets for new developments in precision medicine. Biobanks are more than infrastructures providing HBS and associated data. Biobanks have pioneered in identifying and standardizing sources of preanalytical variations in HBS, thus paving the way for the current biospecimen science. To achieve this milestone, biobankers have successively assumed the role of "detective," and then "architect," to identify new detrimental impact of preanalytical variables on the tissue integrity. While standardized methods in omics are required to be practiced throughout research communities, the accepted best practices and standards on biospecimen handling are generally not known nor applied by researchers. Therefore, it is mandatory to raise the awareness within omics communities regarding not only the basic concepts of collecting, storing, and utilizing HBS today, but also to suggest insights on biobanking in the cancer omics context.

Transcriptional landscape of mouse-aged ovaries reveals a unique set of non-coding RNAs associated with physiological and environmental ovarian dysfunctions

The progressive and physiological decline in ovarian function depends on the rate of follicular loss by atresia, contributing to the reduction in ovarian reserve. Genetics and environmental factors play important roles in ovarian senescence and in the onset of ovarian dysfunctions such as diminished ovarian reserve. A better understanding of the mechanisms underlying ovarian aging and their regulation by genetic and environmental factors is needed to evaluate ovarian reserve and to predict fertility potential by identification of more accurate and less invasive markers. We report transcriptomic data (i) implicating novel (e.g. EIF2 signalling) and well-known pathways (e.g. TGFβ signalling), and (ii) defining a unique set of non-coding RNA (ncRNA), both associated with ovarian function. The latter includes miRNAs (e.g. Mir143 and Mir145), snoRNAs (e.g. Snord16a and Snora34), and one lncRNA (Gas5), which are differentially expressed in middle-aged ovaries (12 months) vs young-aged (3 months) from CD1 mice. Experimental analysis confirms that ovary lifespan varies across genetic backgrounds in mice and, genetics influences the response to environmental perturbations such as diet. Moreover, the identified ncRNAs were verified in a model of reproductive dysfunction promoted by the environmental toxicant ethylenthiourea. We also report the increase of miRNA143 and miRNA145 in follicular fluid of women with diminished ovarian reserve. Their levels inversely correlate with the hormonal profile and with the number of the oocytes recruited upon hormonal stimulation. Overall, we report a transcriptomic signature for ovarian dysfunction in vivo that provides a valuable resource for translational research in human reproductive aging.

Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers

Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.

The hypoxia marker CAIX is prognostic in the UK phase III VorteX-Biobank cohort: an important resource for translational research in soft tissue sarcoma

Background:Despite high metastasis rates, adjuvant/neoadjuvant systemic therapy for localised soft tissue sarcoma (STS) is not used routinely. Progress requires tailoring therapy to features of tumour biology, which need exploration in well-documented cohorts. Hypoxia has been linked to metastasis in STS and is targetable. This study evaluated hypoxia prognostic markers in the phase III adjuvant radiotherapy VorteX trial.Methods:Formalin-fixed paraffin-embedded tumour biopsies, fresh tumour/normal tissue and blood were collected before radiotherapy. Immunohistochemistry for HIF-1α, CAIX and GLUT1 was performed on tissue microarrays and assessed by two scorers (one pathologist). Prognostic analysis of disease-free survival (DFS) used Kaplan–Meier and Cox regression.Results:Biobank and outcome data were available for 203 out of 216 randomised patients. High CAIX expression was associated with worse DFS (hazard ratio 2.28, 95% confidence interval: 1.44–3.59, P<0.001). Hypoxia-inducible factor-1α and GLUT1 were not prognostic. Carbonic anhydrase IX remained prognostic in multivariable analysis.Conclusions:The VorteX-Biobank contains tissue with linked outcome data and is an important resource for research. This study confirms hypoxia is linked to poor prognosis in STS and suggests that CAIX may be the best known marker. However, overlap between single marker positivity was poor and future work will develop an STS hypoxia gene signature to account for tumour heterogeneity.

Patient-Centered Network of Learning Health Systems: Developing a resource for clinical translational research.

The Learning Health System Network clinical data research network includes academic medical centers, health-care systems, public health departments, and health plans, and is designed to facilitate outcomes research, pragmatic trials, comparative effectiveness research, and evaluation of population health interventions. The Learning Health System Network is 1 of 13 clinical data research networks assembled to create, in partnership with 20 patient-powered research networks, a National Patient-Centered Clinical Research Network. Herein, we describe the Learning Health System Network as an emerging resource for translational research, providing details on the governance and organizational structure of the network, the key milestones of the current funding period, and challenges and opportunities for collaborative science leveraging the network.

Brain tumor biobanking in the precision medicine era: building a high-quality resource for translational research in neuro-oncology.

The growth of precision medicine has made access to biobanks with high-quality, well-annotated neuro-oncology biospecimens critical. Developing and maintaining neuro-oncology biobanks is best accomplished through multidisciplinary collaboration between clinicians and researchers. Balancing the needs and leveraging the skills of all stakeholders in this multidisciplinary effort is of utmost importance. Collaboration with a multidisciplinary team of clinicians, health care team members, and institutions, as well as patients and their families, is essential for access to participants in order to obtain informed consent, collect samples under strict standard operating procedures, and accurate and relevant clinical annotation. Once a neuro-oncology biobank is established, development and implementation of policies related to governance and distribution of biospecimens (both within and outside the institution) is of critical importance for sustainability. Proper implementation of a governance process helps to ensure that the biospecimens and data can be utilized in research with the largest potential benefit. New NIH and peer-reviewed journal policies related to public sharing of 'omic' data generated from stored biospecimens create new ethical challenges that must be addressed in developing informed consents, protocols, and standard operating procedures. In addition, diversification of sources of funding for the biobanks is needed for long-term sustainability.

Abstract A03: Analyses of a prostate cancer patient-derived xenografts series, a resource for translational research

Abstract Patients with metastatic prostate cancer (PCa) have effective therapy options, but none of them are curative. Thus, their mortality rates are persistently high. Essential to furthering our progress in PCa research and therapy development is a spectrum of models that reflect the heterogeneity of the disease at each tumor site as well as the different histological variants of PCa (e.g., adenocarcinoma, small cell carcinoma). To address this challenge, we developed a strategy to establish PCa patient-derived xenografts (PDXs), using PCa tissue specimens taken from PCa sites demonstrating clinical progression. This approach provided a diverse repository of PDXs that can be linked prospectively with clinical progression and led to the identification of clinically relevant therapy targets and have proven valuable for testing drugs. We studied the first 50 PDXs developed under our program to a) define the histopathological features of paired human PCa and corresponding PDXs applying the clinically defined morphological characterization groupings of human cancer to the PDX tumors; b) assess the expression of genes known to play roles in PCa pathogenesis (e.g., androgen receptor, PTEN, ETS gene fusions) in PDXs and the human tumors of origin using immunohistochemistry and fluorescence in situ hybridization and c) perform array comparative genomic hybridization to 42 PDXs. We found that the histopathological and molecular pattern of these PDXs maintain the fidelity with the human tumor of origin. Furthermore, of the 50 cases studied, 32 (64%) were adenocarcinomas, and 16 (32%) were small cell carcinomas, poorly differentiated neuroendocrine carcinomas or mixed adenocarcinoma/ small cell carcinomas. In our cohort, we also have one sarcomatoid tumor and one ductal adenocarcinoma. Of the 32 adenocarcinomas in this cohort, 26 were AR-positive (81%), and 11 of the 27 AR-positive adenocarcinomas (41%) had aberrant expression of genes frequently involved in recurrent rearrangement (e.g., ERG, ETV1, ETV5). Also, SCCs and poorly differentiated neuroendocrine carcinomas did not express AR and were negative for ERG. This distribution recapitulates that of human PCa in the general population. Comparative genomic hybridization demonstrated gains and losses previously reported in PCa with a defined cluster of genomic aberrations. Significant differences in oncogenic pathways activation in pairs of PDXs derived from different areas of the same tumor suggesting divergent cellular progression. Finally, using this platform, we identified a focal deletion of speckle-type POZ protein-like (SPOPL) gene in 7/28 PDX. SPOPL is a MATH-BTB protein that shares an overall 85% sequence identity with SPOP (a SPOPL paralog). SPOP was recently reported to be mutated in about 8% of PCa and to define a molecular subclass of PCa. No mutations were found in SPOP in our cohort. In support of our findings, deletions on SPOPL were also found in about 7% of the PCa in TCGA data suggesting that our cohort is a reliable platform for discovery. In conclusion, we have developed a dynamic repository of clinically annotated samples that can be used as a discovery platform. Furthermore, these clinically annotated samples can be linked prospectively to clinical progression/response to therapy and thus will help define therapeutic targets for subpopulations of men and to identify likely responders to previous and upcoming therapies. Citation Format: Nallasivam Palanisamy, Jun Yang, Xinhai Wan, Elsa M. li Ning Tapia, John C. Araujo, Eleni Efstathiou, Estefania Labanca, Louis Pisters, Ana Aparicio, Ritu Bhalla, Scott Tomlins, Lakshmi P. Kunju, Arul Chinnaiyan, Christopher J. Logothetis, Patricia Troncoso, Nora M. Navone. Analyses of a prostate cancer patient-derived xenografts series, a resource for translational research. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr A03.