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University of Texas Southwestern Medical Center
University of Texas SPORE in Lung Cancer (P50CA70907) John D. Minna, M.D. Principal Investigator (UTSW) University of Texas Southwestern Medical Center, Dallas, TX University of Texas SPORE in Lung Cancer: A Collaboration Between The University of Texas Southwestern Medical Center (UTSW) and The University of Texas M. D. Anderson Cancer Center (MDACC). The strategic plan of this SPORE is to identify and understand the molecular "hallmarks of lung cancer" and then translate this information into the clinic for early detection, prevention, prognosis, and the selection and/or development of new treatments for lung cancer. We have invested in several major translational research themes: identification of key lung cancer tumor suppressor genes and their development as novel therapeutics; identification of persons with an increased inherited and/or acquired risk of developing lung cancer by genetic epidemiology and early detection of respiratory epithelial genetic and epigenetic alterations; identification of abnormalities in apoptosis and invasion during lung cancer pathogenesis; understanding signaling pathways that are likely new targets for chemoprevention and therapy of lung cancer; and developing lung cancer therapies directed against telomerase. To achieve these goals, our SPORE has assembled clinicians and basic scientists including medical oncologists, thoracic surgeons, pulmonary physicians, pathologists, molecular geneticists, molecular and cell biologists, epidemiologists, behavioral and psycho-pharmacologists, biostatisticians, and experts in development of new technologies and informatics. The SPORE, brings together two major complementary strengths in lung cancer research involving UTSW and MDACC. This SPORE consists of 5 inter-related projects and 4 supporting Cores. The projects involve: 1. Translation of tumor suppressor genes into new therapeutics for lung cancer; 2. Molecular epidemiology of lung cancer: comparison of surrogate and target tissues markers; 3. Molecular pathology of lung cancer related to apoptosis and invasion and its translation into the clinic; 4. The PI3K pathway as a target for lung cancer prevention and therapy ; and 5. Targeting telomerase for lung cancer therapeutics The Cores are: (A) Administrative; (B) Pathology & Tissue Resources; (C). Biostatistics; and (D) Computational Biology & Innovative Technology. All of the scientific projects are: translational in nature; focus on human lung cancer; involve clinical and basic investigators and biostatisticians; interact with the other projects; and utilize Core resources. Innovative Developmental and Career Development Projects have brought new investigators into and stimulated the SPORE that are represented in each of the major projects. We also have a developmental project dealing with new methods of smoking cessation by elucidating genetic contributions to nicotine addiction and response to pharmacological treatment of nicotine addiction. This SPORE also participates in the inter-SPORE effort of the Lung Cancer Biomarkers and Chemoprevention Consortium (LCBCC). Achievement of the aims and objectives of this proposal will result in a major decrease in the incidence, morbidity and mortality of lung cancer. This a joint effort between The University of Texas Southwestern Medical Center and The University of Texas M. D. Anderson Cancer Center. Project 1 Allelic losses on chromosome arm 3p are the most frequent and earliest genetic abnormality detected in human lung cancers, indicating the presence of one or more lung cancer tumor suppressor genes (TSGs) in this region. In particular, a 600-kb lung cancer homozygous deletion region at 3p21.3 shows frequent allele loss in tumors and smoking-damaged lung epithelium. We identified a group of 23 candidate TSGs in this small 600-kb 3p21.3 region, several of which occasionally suffer mutations, but no one gene was targeted. Several ( CACNA2D2 , BLU , RASSF1A isoform, and SEMA3B ) had their expression extinguished related to tumor-acquired promoter DNA methylation. Using a variety of expression vectors, we found that several of the candidate 3p21.3 TSGs, FUS1 , 101F6 , NPRL2 , and SEMA3B , effectively inhibited tumor cell growth by induction of apoptosis in vitro and in vivo, while others, RASSF1A and CACNA2D2 , efficiently inhibited anchorage-independent growth in vitro and xenograft growth in vivo without inducing apoptosis ( RASSF1A ) or inducing apoptosis only in p53 wild-type tumors ( CACNA2D2 ), strongly suggesting that several of these contiguous 3p21.3 genes function as lung cancer tumor suppressors. The purpose of this project is to gain a comprehensive understanding of the molecular mechanisms and biological pathways of the products of the 3p21.3 genes alone and in combination with each other and other TSGs with the goal of developing these genes into new therapeutics and diagnostics. The Specific Aims are 1. to confirm the loss of expression of these genes and the timing of this loss in lung cancer pathogenesis by immunohistochemical analysis of tumor and preneoplastic tissues using tissue microarrays (TMAs) and new proteomics tools (ProteinChip, Ciphergen Biosystems, Fremont, CA) to study modifications of their proteins in these samples; 2a. to determine the molecular changes and cellular responses (particularly induction of apoptosis) in human NSCLC cells mediated by re-expression of these 3p21.3 genes, p53, and FHIT using mRNA (microarray) expression profiling and SELDI-Mass spectrometry analysis-based protein profiling; 2b. to confirm the role of these 3p21.3-encoded proteins as tumor suppressors by knocking down their expression using siRNA technology in normal human epithelial cultures and then studying the resultant mRNA and protein expression profiles and testing for the development of the malignant phenotype; 3. to quantitatively evaluate interactions of the 3p21.3 genes in combination with each other and with p53 or FHIT for their tumor-suppressing activities in vitro and in vivo ; 4. to conduct a series of Phase I clinical trials to evaluate these genes (starting with FUS1 ) as therapeutic agents delivered systemically using a DOTAP:Chol lipoplex. By studying the same materials as SPORE Projects 2 and 3, we will be able to integrate the data from the different projects. Thus, this project has a "pipeline" of candidate TSGs that we propose to bring through preclinical tests into clinical therapeutic trials singly or in combination as new therapies for lung cancer; the project will interface with other SPORE Projects to exploit information obtained from the trials for diagnosis, prognosis and risk assessment purposes. This a joint effort between The University of Texas Southwestern Medical Center and The University of Texas M. D. Anderson Cancer Center. Project 2
Although lung cancer is often considered an environmentally induced disease related to smoking, increasing evidence support the hypothesis that lung cancer is in part determined by genetic factors. The main goal of this project is to ultimately discover genetic markers that identify those persons at highest risk for developing lung cancer after accounting for smoking exposure. The translational application of these findings will be used to identify genetic epidemiology markers applicable to early lung cancer detection, risk assessment, and thus identifiy individuals most suitable for lung cancer screening and chemoprevention trials.
Project 3 Our previous SPORE project identified several genes silenced during the multistage pathogenesis of lung cancer, and methylation of six of these are being tested as intermediate markers of response in chemoprevention trials. In this proposal we will build on this theme, and we will study the clinico-pathological significance of evasion of apoptosis and tumor invasion, two of the hallmarks of lung cancer. Our proposal combines the cell biology/pathology expertise of Adi Gazdar with the apoptosis experience of Preet Chaudhary and will be supported by collaborators at the British Columbia Cancer Agency, Vancouver. Deregulation of apoptosis occurs at multiple levels of the death receptor and mitochondrial pathways Over-expression of the catalytically inactive caspase 8 homologue c-FLIP is not only anti-apoptotic, but also associated with drug resistance to lung cancer cells. Loss of cell adhesion cadherin molecules CDH1 and CDH13 and the crucial integrin-laminin combination (five independent genes) that anchors epithelial cells to the basement membrane are frequent in lung cancers. The latter is of special importance as it represents the very first step in tumor invasion. Deregulation of these genes occurs by aberrant methylation and by other mechanisms. After testing expression of over 50 molecules, we selected 20 for initial detailed study, using assays for methylation (methylation specific PCR and real time PCR) and protein expression (Western blots and immunostains), and another 10 molecules will be identified and studied during the course of this proposal. In Aim 1 we will identify 30 genes whose expression is deregulated by testing panels of lung cancer cell lines and tumors. In Aim 2 we will determine if aberrant methylation is the mechanism of silencing of these 30 genes and we will establish and validate methylation specific and real time PCR assays for them. Aim 3 will determine when deregulation of these molecules occurs during the multistage pathogenesis of lung cancer, so as to determine whether they can be used as intermediate markers for chemoprevention studies. In Aim 4 we will study 300 well-characterized resected NSCLCs to determine if deregulated expression of these molecules, either individually or in combination, is correlated with survival or multiple other clinico-pathological features. We will utilize resources from all of the Cores and interact with two other projects. Translational aspects include identification of markers for prognosis, chemoprevention and risk assessment. Our studies will greatly aid the understanding and clinical application of two crucial hallmarks of lung cancer. This a joint effort between The University of Texas Southwestern Medical Center and The University of Texas M. D. Anderson Cancer Center. Project 4 To date, all trials of lung cancer chemoprevention agents performed in the United States and Europe have failed to show that this therapy confers a benefit to individuals at increased risk of developing lung cancer. Most of these trials examined the chemopreventive efficacy of retinoid-based regimens. Through studies performed under our current SPORE grant, which evaluated mechanisms of retinoid response and resistance in human bronchial epithelial (HBE) cells, we showed that retinoids suppress the proliferation of HBE cells by inhibiting the activity of mitogen-activated protein (MAP) kinase pathways and that retinoids do not inhibit MAP kinase pathways in non-small cell lung cancer (NSCLC) cells, which are resistant to the growth inhibitory effects of these agents. These findings indicated that activation of specific kinase pathways is crucial to maintaining the proliferation and survival of normal and neoplastic HBE cells. Based on this novel observation, we began to explore the activity of other kinase pathways in normal and neoplastic lung tissues. We have evidence that the phosphatidylinositol 3-kinase (PI3K) pathway is activated in bronchial premalignancy and NSCLC. Further, inhibition of the PI3K pathway inhibits the growth of NSCLC cells. The biologic effects of PI3K pathway inhibitors on NSCLC cells varied depending on the specific components of the cell that were inhibited; inhibition of either PI3K or cJun N-terminal kinase (JNK), which is activated by PI3K through RAC-1, induced proliferative arrest, whereas combined inhibition of PI3K and JNK induced apoptosis. We hypothesize that because activation of the PI3K pathway is crucial for transformation of HBE cells to bronchial premalignancy and subsequently for survival of NSCLC cells, targeting the PI3K pathway will be effective in preventing lung cancer and treating clinically evident disease. The goal of our SPORE competitive renewal is to develop lung cancer chemopreventive and treatment approaches that target the PI3K pathway and induce apoptosis of bronchial premalignancy and lung cancer cells. We propose to investigate the efficacy of inhibitors of the PI3K- and JNK-dependent pathways that are currently in various stages of preclinical and clinical development in lung cancer prevention and therapy using multiple complementary preclinical models, including an in vitro lung carcinogenesis model (Aim 1) and three animal models of human lung cancer (Aim 2). We will investigate the importance of inhibiting the PI3K pathway in the chemopreventive actions of ZD1839, an inhibitor of the ErbB1 tyrosine kinase, in a clinical trial targeting individuals at high lung cancer risk (Aim 3). We will translate findings from these studies into the clinic by developing a clinical trial to investigate the lung cancer chemopreventive or therapeutic efficacy of the novel PI3K pathway inhibitors investigated in Aims 1 and 2. This a joint effort between The University of Texas Southwestern Medical Center and The University of Texas M. D. Anderson Cancer Center. Project 5 The correlation between telomerase activity and the growth of human tumors has led to the hypothesis that continuous growth of advanced malignancies requires reactivation of telomerase. Hence, inhibitors of telomerase may represent a novel approach to cancer therapy. Here we propose to use oligonucleotides complementary to the RNA domain of telomerase to investigate antitelomerase therapeutic strategies and initiate clinical trials of antitelomerase therapy. Beginning trials will be facilitated by the fact that chemically similar oligonucleotides (but against different targets) are now being evaluated in lung cancer clinical trials. One of these compounds, ISIS 3521 has produced promising survival benefits when combined with systemic chemotherapy in patients with advanced non-small cell lung cancer (NSCLC). The use of oligonucleotide approaches to inhibit telomerase in lung cancer has not been reported. Telomerase RNA is not a typical antisense target and offers many advantages relative to mRNA targets because its essential catalytic core is readily accessible to oligonucleotide binding. We have access to highly potent inhibitors from both Geron Corporation and ISIS Pharmaceuticals and will proceed into clinical trials with the inhibitor that appears to possess the most favorable properties based on our pre-clinical investigations. Both the Geron and ISIS compounds belong to families of oligonucleotides that possess improved pharmacokinetics. In addition to large-scale syntheses, these inhibitors are highly resistant to nucleases, are water soluble, acid resistant, and display high thermal stability of duplexes formed with RNA strands. The overall pre-clinical specific goal of this project is to combine chemistry and cell biology in an integrated effort to evaluate the effects of inhibiting telomerase with targeted oligonucleotides in lung tumors both in cell culture and in mice with tumor xenografts. Promising agents will complete studies of drug formulation and safety profile, experimental pharmacokinetics and animal toxicology in collaboration with our pharmaceutical partners to guide the conduct of clinical trials. Although it is expected that telomerase inhibitors will be most effective when treating minimal residual disease, we will focus first in advanced human disease by examining whether telomerase inhibitors work additively or synergistically with standard chemotherapy. We anticipate conducting Phase I clinical and pharmacologic studies of promising antitelomerase inhibitors alone followed by combinations with chemotherapeutic agents in patients with advanced NSCLC with malignant pleural effusions. This strategy will allow us to test the efficacy of inhibiting telomerase in humans as well as determining potential side effects and best treatment schedule. These studies will be followed by Phase II efficacy trials in patients with advanced NSCLC. We anticipate these studies to provide clinical evidence on the importance of inhibiting telomerase to improve patient response and survival. This a joint effort between The University of Texas Southwestern Medical Center and The University of Texas M. D. Anderson Cancer Center. Core 1 The Administrative Core Responsibilities include:
Core 2 The Pathology and Tissue Resources Core will provide routine and innovative tissues and materials essential for achieving the aims of the SPORE projects. Routine materials include tumors and non-malignant lung specimens and tumor cell lines. Over 2,000 tumors and 200 cell lines have been banked, and over 4000 aliqouts of tumor or cell line pellets, RNA or DNA or paraffin sections have been distributed to SPORE investigators. Our Aim 1 is to collect, process, store, catalog and distribute routine tissues, both malignant and non-malignant, and relevant data as requested by the various component projects of the SPORE. The tumors fall into three categories. Group one, which constitute our "gold standard" specimens, are from patients from whom extensive materials, clinico-pathological, familial, smoking, carcinogen exposure and other information are available. Over 100 of these cases exist currently, and 75 further cases will be added per year. At the end of the proposal, about 300 of these cases will have at least three years of follow up information. The other categories contribute larger numbers of tumors including small cell lung cancer (SCLC), carcinoids, mesotheliomas, tumors from never smokers and from other countries. Aim 2 is to develop and utilize innovative or unique resources that will aid in the successful completion of the SPORE aims. Innovative materials consist of a) tissue microarrays from our group one cases, b) cell lines from paired SCLC tumors before therapy and at relapse; c) cell lines from paired primary and metastatic NSCLC tumors; c) short term lung cancer cultures consisting of almost pure tumor cells for microarray and CGH studies; d) cell line microarrays suitable for immunostaing and FISH analyses; e) cultures of immoratalized but non-tumororigenic bronchial epithelial cultures from smokers and never smokers; f) harvests of non-cultured pure epithelial bronchial cells; and g) a bank of 160 preneoplastic biopsies. Aim 3 is to distribute resources and reagents to SPORE investigators and others. Four of our five projects witll utilize CORE materials. Heavy utilization of our routine and innovative materials, and close interactions with the SPORE investigators will greatly aid the successful completion of the aims of our SPORE proposal. Core 3 The research proposals in the SPORE encompass a broad range of activities, including studies in cell lines, animal models, and clinical trials. These studies will generate a number of different types of data. In order to design and analyze such a wide variety of studies properly, a variety of mathematical techniques will be required. In addition, a strong data management system is vital to the operation of the SPORE. If Projects are to cooperate efficiently, they must have access to relevant data. The data must be easily accessible, but stored in a secure manner with assurance of patient confidentiality. Data and information must flow smoothly between projects. Data quality and integrity must be assured by data audit and backup procedures. In addition, there needs to be an efficient interface between the computational biology and data storage facilities provided by SPORE Core D (Innovative Technology, Computational Biology and Microarray Core). This is particularly true for the large amounts of microarray and proteomics expression profiling information. In order to meet these needs, the Biostatistics/ Informatics Core therefore brings together a number of biostatisticians and biomathematical scientists with expertise in a number of statistical and data management disciplines. By placing these personnel within the Biostatistics/Informatics Core rather than in individual Projects, the ability of the Projects to interact is strengthened. Thus, the Biostatistics/Informatics Core will provide expertise in study design, data analysis, and data management to all Projects and Cores. The specific aims of the Biostatistics and Informatics Core are: 1. to provide the statistical design and analysis required to achieve the specific aims of each project; 2. to assist in the design, evaluation, and analysis of new research arising from the individual projects, the Developmental Projects, and the Career Development Trainees; 3. to provide database support and expertise for the collection, storage, and retrieval of clinical data, including provisions for quality assurance, auditing procedures, and patient confidentiality; 4. to assist the other Cores and Projects in the collection, entry, and maintenance of data specific to those Cores and Projects. In this regard, to interface with the Innovative Technology/Computational Biology/Microarray Core (SPORE Core D) in providing biostatistical analysis and assistance with data warehousing of the microarray and proteomics data; and 5. to coordinate the data acquisition and biostatistical analysis and audit planning for the Administrative Core.
Core 4 The goal of the Innovative Technology, Computational Biology, and Microarray Core is to continue to develop new technologies and data analysis mining tools in support of the projects of this SPORE and then deploy these enabling technologies against the needs of all of the SPORE projects and other Cores. This Core will help SPORE investigators to gather complete data sets on laboratory and clinical samples, interface these datasets with the SPORE Biostatistics & Informatics Core (Core C), and then assist SPORE investigators and the Biostatistics Core in the interpretation of these data using data mining techniques. The instrumentation-based technologies include microarrays and methods for expression, sequence variation, methylation and other epigenetic measurements, and proteomics diagnostics. Other facilities include educational modules/classes, identification/testing of new technologies/methods of potential value to all SPORE researchers, and the large complement of computational codes and databases made available on our servers at http://innovation.swmed.edu . Software, available over the web or via downloadable modules for the analysis of expression data, genomics experimental design, text mining and DNA sequence analysis has been produced and is in daily use by SPORE researchers. The Specific Aims of Core D are: 1.) To develop applied computational biology resources - codes, databases and interpretations of data - to facilitate advances in translational lung cancer research and to provide computational support for SPORE investigators; 2.) To perform oligonucleotide based microarray mRNA expression profiling and ProteinChip SELDI-Mass spectrometry based protein expression profiling and proteomics analysis, planned and analyzed jointly with SPORE project investigators and the SPORE Biostatistics/Informatics Core. We will develop and refine these technologies along with other new innovative technologies, such as array based DNA methylation and CGH analysis, and array based re-sequencing technology for the analysis of cancer, normal tissues, pre-neoplastic lesions, and tumor-derived cell lines. We will collaborate with SPORE investigators on an intra and inter-SPORE basis to apply these technologies to lung cancer translational research; 3.) To construct an internet accessible, www-based ( http://spore.swmed.edu ) SPORE Bioinformatics tool set and data warehouse of utility and available to facilitate intra and inter-SPORE collaborations and particularly to facilitate the interaction of the Biostatistics/Informatics Core and SPORE investigators with their databases. We will establish and maintain computer servers to support this effort; 4.) To develop and maintain a Lung Cancer SPORE web site ( http://spore.swmed.edu ) to facilitate research, exchange of information and ideas among SPORE investigators for intra and inter-SPORE collaborations and with SPORE advisors. The above cores are joint efforts between The University of Texas Southwestern Medical Center and The University of Texas M. D. Anderson Cancer Center. List of Investigators John D. Minna, M.D. Jack A. Roth, M.D. Christopher I. Amos, Ph.D. E. Neely Atkinson, Ph.D. Keith A. Baggerly, Ph.D. B. Nebiyou Bekele, Ph.D. Nancy Caraway, M.D. Preet M. Chaudhary, M.D., Ph.D. Kevin R. Coombes, Ph.D. David R. Corey, Ph.D. J. Michael Dimaio, M.D. Jonathan E. Dowell, M.D. William H. Frawley, Ph.D. Boning Gao, Ph.D. Harold (Skip) Garner, Ph.D. Adi F. Gazdar, M.D. Lin X. Ji, Ph.D. Feng Jiang, M.D., Ph.D. Ruth L. Katz, M.D. Jonathan M. Kurie, M.D. Stephen Lam, M.D., FCPC Calum MacAulay, Ph.D. Tim McDonnell, M.D., Ph.D. Sara Milchgrub, M.D. Gordon B. Mills, M.D., Ph.D. Joe B. Putnam, Jr., M.D. Jerry W. Shay, Ph.D. Margaret Spitz, MD, MPH Gail E. Tomlinson, MD, Ph.D. Garrett L. Walsh, M.D. R. Allen White, Ph.D. Ignacio Wistuba, M.D. Xifeng Wu, M.D., Ph.D. |
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